About half the Army's new Apache attack helicopters, bought for £3bn, will have to be taken out of service for up to four years because pilots cannot be trained in time to fly them, the Whitehall spending watchdog warns today.

The National Audit Office said that although the aircraft were being delivered on time, a private finance initiative deal to train the aircrew was three years behind schedule. Dozens of aircraft would have to be stored in hangars because the completion date for the initial training programme for 144 pilots had been put back from April 2004 to February 2007.

The NAO warned that the delay in training had put in jeopardy the delivery of the first fully equipped regiment of 16 Apaches, scheduled for February 2005. It said the Army could face a "significant capability gap" because the life of the TOW wire-guided missiles on its ageing Lynx helicopters could not be extended.

The NAO also said contractual problems over the supply of spares meant that the Apaches kept in storage may have to be cannibalised for parts so that other aircraft could carry on flying.

When the initial order for 67 Apaches was placed with Westland Helicopters in 1995, its combination of firepower and manoeuvrability was said to offer the biggest enhancement of the Army's fighting capability since the introduction of the tank.

Originally it had been intended that Westland, as the prime contractor, would also supply the training, but the MoD decided that the deal on offer was "unaffordable". Instead a separate PFI agreement was reached with Atil – a company jointly owned by Westland and the Apache's US manufacturer Boeing – which was supposed to save £23m.

But it was beset with problems. The hi-tech flight simulator ran into technical difficulties which delayed delivery by 17 months and meant pilot training, originally scheduled for 2001, will not now start until September next year.

At the same time the duration of the training courses has had to be extended from 15 weeks to 26 weeks – in part because the helicopter is now much more sophisticated than had been originally envisaged.

However the original programme was based on the experience of the US Army, which trains in Alabama, and failed to take account of the fact that many more flying days are likely to be lost to poor weather in the UK. As a result, the NAO said that between 2002 and 2006, a "large number" of Apaches – some estimates say more than half – would have to be stored away in hangars at RAF Shawbury in Shropshire at a cost of £6m.

Already, 11 of the 25 helicopters so far delivered have been put into storage.

Although the PFI deal was supposed to save money, the MoD had to write off £34m due to the cancellation of maintenance courses because Westland failed to deliver the training material on time.

The NAO also revealed the first Apache crews would have no secure radio communications with British ground troops or other helicopters – although they would be able to speak to the Americans – because of delays to the Army's Bowman radio system.