For two weeks the phone at St Stephen Walbrook, the Wren church in the City of London, has remained unanswered. I arrive for the weekly sung Eucharist on a Thursday lunchtime, hoping to catch its famous rector that way. But the Rev Chad Varah is not taking the service. He hasn't for several weeks, since becoming unwell. Varah, the founder of the Samaritans, which celebrates its 50th anniversary in November, turns 92 that same month.

I am shown into the vestry, a comfortably disordered affair. On one wall is a pinboard covered in yellowing newspaper headlines featuring the word "Chad"; they refer not to the clergyman (named after the seventh-century saint), but to the African country. "Libyan jets mass for Chad battle" says one. On the opposite wall is a framed award from the American Association of Suicidology for "outstanding contributions in the area of suicide prevention". The floor bears no visible reminder of the time when a woman who came to Varah distressed about her life-long desire to "piss on the carpet" took him up on his suggestion that she do so there and then.

A warden calls Varah (who claims the title of Britain's oldest sex therapist) on an old black telephone on the crowded desk. Varah agrees to talk to me, but insists we do the interview immediately, rather than at his home, as he says he doesn't know whether he'll still be alive the following week. The rector, who has been diagnosed with cancer and also has osteoporosis, barks at me when I say I'm sure he will be. Varah very much wants to talk: about the organisation he founded and worked for for 33 years, and specifically about how he no longer has any respect for it; so much so that this year he asked the Charity Commission to take away its charitable status.

Varah's first task as an assistant curate in Lincoln in 1935 eventually led him to set up the world's first telephone hotline and drop-in centre for the suicidal and despairing. The vicar was unwell and Varah was asked to stand in at the funeral of a 13-year-old girl. When he asked the undertaker why the burial was taking place in unconsecrated ground, he was told that the death had been a suicide. "I was shattered," Varah remembers. "I said, 'Suicide at 13? Why?' A silly question, I know."

The undertaker said the girl had told his daughter that she had begun to bleed between the legs and thought it was a horrible disease. She had not understood that she had started menstruating, and neither had the undertaker's daughter. There was no one to whom the girl felt she could turn. "When I got to the graveside I performed the service as quickly as I could so the mourners could get back under cover as it was raining," Varah says. "It was my first day and I didn't want to have to cope with the child's relatives. I stood at the end of the grave and I said, 'Little girl, I never knew you, but I promise you that you have changed my life and I shall teach children about sex even if I get called a dirty old man at the age of 24.'"

That night he kept his vow, explaining at the church youth club the sexual meaning of the word "sod", which one of the girls had used. He continued to educate the children whenever they asked about sex. Varah, a vicar's son and Oxford graduate, was not yet married (though he had had "unspecified sexual relations" before he was ordained). He himself had been told the facts of life at the age of 12 by a returned missionary bishop who confirmed him. After the chat, Varah felt "slightly relieved to know that masturbation, of which I was a devoted practitioner and had been since before puberty, is a normal manifestation of adolescence", as he wrote in his 1992 autobiography, Before I Die Again (he believes in reincarnation).

In preparation classes for marriage, the clergyman started briefing young couples on how to achieve a "happy and successful" sex life, informing them that the clitoris was a "gift of God" to enable women to enjoy sexual satisfaction, with or without a partner, and that "any husband who was dubious about the effort involved could simply be labelled as one who didn't know as much about sex as the vicar".

It was while vicar of St Paul, Clapham, in south London, where he moved in 1949, that Varah noticed "that amongst people coming to see me with sexual problems, very many of them were talking about suicide. I thought what a good idea it would be if there was a special number on the telephone if you needed information about sex or why you shouldn't commit suicide. I said: 'God, don't look at me, I'm too busy.' It would need someone in the City, where there are 40 Anglican churches in a square mile, and it had to be someone's speciality."

Varah was not only married by this time, but a father of five (including triplets). He was also chaplain of St John's Hospital, Battersea, staff scriptwriter/visualiser for the Eagle and Girl strip-cartoon magazines and, bizarrely, scientific and astronautical consultant to the Dan Dare strip.

Not long afterwards, he was invited by the Worshipful Company of Grocers of the City of London to apply for the benefice of St Stephen Walbrook. "I told them about my mad scheme for setting up a special telephone for suicidal people and an open door for people who wanted to see me. I thought that would put them off. On the contrary: they wanted done what I wanted to do."

The telephone number of the church was publicised in the press and Varah, with the help of just a secretary, launched the project on 2 November 1953. His first call was from a destitute mother of four about to be evicted, who had decided to kill her children and herself. Varah rushed to her, and all the threatened lives were saved. Soon, volunteers began turning up at the church to help, talking to the clients as they waited to see Varah. He realised they were doing the clients great good simply by listening as they talked themselves out of trouble. Only a minority needed counselling from Varah or referral to a psychiatrist.

On 2 February the following year, Varah called the volunteers together and told them that he would be leaving the phone-answering and befriending to them, and he would supervise and see clients who needed counselling. In 1959, a second branch was opened, in Edinburgh. Ten years after its inception, there were 41 branches in the UK and the Republic of Ireland.

On the Samaritans' 21st anniversary - 2 November 1974 - Varah stepped down as director of the London branch and became chairman (and later president) of Befrienders International, which he founded as the worldwide body of the Samaritans. He continued as rector of St Stephen Walbrook and as a sex therapist, his "specialisation" being women unable to orgasm. Not everyone thought such work fitting; in the early 1970s, he was arraigned before the Deanery Synod on a charge of conduct unbecoming a clergyman because of his association with Forum magazine, for whom he wrote articles such as "Let them be gay", "The right to abortion" and "Is marriage still valid?" The motion was defeated.

Varah travelled round the world twice a year for nine years, visiting branches and "teaching how to prevent suicide by befriending, which means listening to people and giving them moral support and encouragement and making them feel good about themselves".

Today, there are 203 branches in the UK and Republic of Ireland. Last year, the charity, which dropped the definite article in its title in order to be seen as more contemporary, received more than 4,600,000 contacts via phone, e-mail, letter, face to face meetings, work in prisons and stands at local fairs and other events.

Part of the Samaritans' success is down to the fact that it is not a religious organisation; Varah always insisted on that. "Many people were driven to suicide because they were too gentle and loveable for the rat race," he says in Before I Die Again. "And where could they find refuge? Who would understand them, and not make them feel inadequate? Not, on the whole, the church. In fact, in a different way, the church's standards were as destructive as the world's standards. Church people were all too often narrow-minded, censorious, judgemental, intolerant, conventional... So the people for whom the world was too harsh would never think of turning to the church, and if they did, they would be likely to feel worse as a result."

On 2 November 1986, Varah retired officially from all Samaritans offices and responsibilities. The following year, the London branch moved out of the crypt at St Stephen Walbrook to bigger premises in Soho. He was appointed an OBE in 1969, a CBE in 1995 and a Companion of Honour in 2000. He was particularly pleased to have been presented with a Pride of Britain lifetime achievement award the same year. "I was delighted because I knew how the Samaritans had rejected me," says Varah.

His feelings of rejection stem from a meeting of the Samaritans' council of management several years ago, where he proposed a series of motions, all of which were defeated. One proposed setting up a committee to look into why so many callers hang up. Another was "to stop people claiming that the 'Brenda system' was encouraging the kind of men who answered ads saying, 'I will make you come in 30 seconds.'" The Brenda system, which was dropped about 20 years ago, allowed sexually frustrated, depressed men to talk on the phone to a volunteer, sometimes to the point where they would relieve themselves, after which they could talk about their problems.

After his motions were defeated, Varah says, he stomped off. "It was the Samaritans leaving me. They were behaving in a totally un-Samaritan way." He says Samaritans is "no longer what I founded. I founded an organisation to offer help, if asked, to suicidal people or equally desperate people. The last elected chairman rebranded the organisation. It was no longer to be an emergency service. It was to be an emotional support group for the whole bloody population whether they wanted it or not." Does he feel hurt? "Would you be hurt if somebody for whom you had no respect rejected you? I don't care what they do or say."

In January this year, Varah wrote to the Charity Commission about the rebranding of Samaritans, asking that the commission take away its status. He was concerned that the service would become overburdened and felt that its purpose would ultimately change. The commission replied that decisions about the charity's practices were at the discretion of its trustees, as long as the practices remained within the charity's agreed objectives.

Lord Palumbo, a close friend of Varah's, says the clergyman feels very hurt. "He founded it, it had a great success rate, the suicide rate dropped [by one-third in England and Wales between 1965 and 1975] and he feels that this is his legacy, which has, in a sense, been betrayed." Varah feels that his founding principles have been either abandoned or adapted in a way that does not reflect his founding mission.

"There is no question that the Samaritans have departed from the principles he laid down. It was always a non-evangelical organisation. I fear that that is now not the case." Some branches abroad, particularly in Australia, have attempted to introduce evangelical elements that Varah finds "thoroughly offensive", Lord Palumbo says.

"The thing about Chad is that he's immensely human. He understands human frailty. I think those two things have accounted for much of his success; apart from having, of course, a brilliant brain, even at his advanced age. He's very, very sharp indeed. His mind is as sharp as it ever was."

Decades of listening to the suicidal and despairing do not appear to have taken their toll on Varah, who is more robust than you might expect. He once said to a client who rang him at home on his day off threatening to kill herself if he didn't change the day of their appointment and leave a note blaming him: "You do that, sweetie, and I'll find out where you're buried and come and piss on your grave."

"He has an inexhaustible inner strength which is able to absorb all these pressures," Lord Palumbo says. "He has tireless energy; or had, until the physical side took its toll. I don't think he's changed, really. He's incorruptible. I think he's a living saint. To have accomplished what he has in 50 years is miraculous. He has been very shoddily treated, I think, by the Samaritans."

Simon Armson, Samaritans' chief executive, says: "We hold Chad in the deepest respect. If it wasn't for him, his vision, his energy, his tireless work, the organisation wouldn't exist and society would be deeply impoverished as a result. Everybody, whether part of the organisation, or people who have benefited from what we provide, or the population as a whole, owes him an enormous debt of gratitude. It's sad when people find that they can't relate to an organisation which might have changed over the years. The organisation is the organisation he founded, but he founded it 50 years ago and time had moved on."

When his strength returns, Varah, whose wife, Susan, died in 1993, will no doubt return to St Stephen Walbrook, travelling from his home in Barnes on public transport. He plans to retire - he is also senior prebendary of St Paul's Cathedral - in December. He has been invited to attend next month's 50th anniversary celebrations at Samaritans' central branch. Friends say he will not be attending.

Samaritans 24-hour confidential helpline: 08457 909090; 24-hour confidential e-mail: jo@samaritans.org