No one could accuse the international aid organisation Médecins sans Frontières of lacking either character or courage. Ever since its foundation more than 30 years ago, its volunteers have attended emergencies when others hesitated to go. Often first on the scene, they have set the standard for preparedness and professionalism in modern aid work. The Nobel Peace Prize it won in 1999 was one of the least contentious on record.

No one could accuse the international aid organisation Médecins sans Frontières of lacking either character or courage. Ever since its foundation more than 30 years ago, its volunteers have attended emergencies when others hesitated to go. Often first on the scene, they have set the standard for preparedness and professionalism in modern aid work. The Nobel Peace Prize it won in 1999 was one of the least contentious on record.

So when MSF announced yesterday that it was pulling out of Afghanistan after a continuous presence there since 1980, this was a decision that it would not have taken without compelling reasons and much heaviness of heart. And the reasons, as set out by MSF yesterday, cast a disturbing light not only on the current situation in Afghanistan, but on the position of aid workers in a country where the foreign military intervention continues - albeit on a much lower level than before and in a generally restricted geographical area.

What MSF said was that its staff were leaving because of security concerns and because of the lack of progress in an investigation into the killing of five of its staff last month. The dangers were underlined again yesterday when at least two election workers were killed in a bomb attack in the south-east of the country - the latest in a growing number of attacks designed to thwart the presidential election planned for October.

The reasons MSF gave for its withdrawal, however, went beyond heightened concern about security. The acute dangers were, after all, why the workers came to Afghanistan in the first place and why MSF was still there. The new element, and the one that MSF clearly regarded as potentially fatal to its mission was something it called "co-optation" of aid work by foreign troops - an allusion to the proliferation of local "reconstruction" teams run by the US military.

Aid organisations have long been wary of working in areas where outside military forces are also engaged in humanitarian assistance. Not because - as the current US National Security Advisor once put it - it is not be the job of the US Marines to accompany children to school, but because non-partisan aid workers, however clearly identified, risk being associated in the minds of the population with troops they regard as hostile. MSF believes that this is why its five workers were attacked. In Afghanistan there is also a belief that the US military is giving (and withholding) reconstruction assistance in return for "co-operation" from the local people. Such conditionality is, rightly, anathema to independent aid organisations, such as MSF, for whom need is the paramount consideration.

That the line between humanitarian and military functions has become blurred in Afghanistan reflects the reality that hostilities there have never really ended - at least not for the Americans, who are still trying to hunt down the al-Qa'ida leader, Osama bin Laden. Also still at war are many Afghans, including resurgent elements of the Taliban and the private militias of regional warlords, who see the foreign forces as invaders and obstacles to their authority.

Lack of security, and the interests of local leaders in exaggerating their power, make it hard to establish the extent to which the regions ouside Kabul are beyond the control of President Karzai. But his frequent pleas for more foreign troops to safeguard the elections, his distrust of his own defence staff, and - as The Independent highlighted yesterday - this year's record poppy crop, which has flourished despite the best efforts of the British military and others to curb it, tell their own story. Kabul may be thriving after its own fashion, but Kabul is but a fraction of Afghanistan.

It is still to be hoped that Mr Karzai's determination, the Afghans' war fatigue and international assistance can combine to produce peace and stability. If, instead, Afghanistan returns to restless warlordism and violence, the withdrawal of MSF will be seen as marking a critical stage in its descent.