The plan to build two 65,000-tonne aircraft carriers for the Royal Navy is now at risk after it emerged that the bill for the warships has risen by £1 billion in the past 12 months alone (Michael Evans writes).

Last night the Ministry of Defence confirmed that the carrier programme was having to be recosted after the decision announced in December to delay construction of the carriers by up to two years. The present cost of the two ships, HMS Queen Elizabeth and HMS Prince of Wales, is £3.9 billion — with another £10 billion for the Joint Strike Fighter aircraft which are being developed for the carriers.

However, according to a memorandum leaked to the BBC, costs have risen sharply as a result of the delay. In December, the Ministry of Defence insisted that the delay would not have significant cost implications.

But with the consortium building the ships now estimating a final bill closer to £4.9 billion, the prestigious programme has become a financial nightmare for the MoD at a time when it is desperately looking for ways of cutting back on the equipment programme.

The memorandum by the board of the carrier consortium — which includes BAE Systems and the VT Group — was written this month.

The memorandum — referring to the two Queen Elizabeth (QE) Class carriers — states: “The MoD will publish its annual report and accounts in July; these will show c£1 billion of QE Class cost growth and the project will come under severe pressure through the opposition and the media.”

It adds: “This is a very real fight for the programme’s survival.”

The disclosure could hardly come at a worse time for the Navy at a time when the defence budget is coming under intense pressure as the Treasury draws up plans to rebuild the public finances in the wake of the recession.

In a speech this month, the head of the Navy, Admiral Sir Jonathon Band, mounted an impassioned defence of the carrier programme, dismissing suggestions they were “Cold War relics” and insisting that Britain would always need such “higher end capabilities”.

In a statement, a MoD spokesman said that they had made clear last year that the cost of the carriers was set to increase.

“The MoD took the decision to delay the two future aircraft carriers in December 2008,” the spokesman said.

“We did this in order to reprioritise investment to meet current operational priorities and to better align the programme with the Joint Strike Fighter aircraft.

“We acknowledged at the time that there would be a cost increase as a result. We are currently re-costing the programme. The MoD accounts published next month will present an initial estimate and the formal costing will be available until later in the year.”

A BAE spokesman said last night that the carrier programme was “progressing well”, with the first steel due to be cut next week.

“The decision to delay the in-service dates of the carriers, taken as part of the MoD’s equipment examination in December 2008 to meet affordability challenges, led to a substantial re-profiling of the programme in order to spread the work over a longer period of time,” the spokesman said.

“It was always clear that this change to the delivery of the ships, announced in March, would lead to an overall increase in costs.

“The whole of the Aircraft Carrier Alliance, of which BAE Systems is one part, is totally committed to delivering the vital strategic capability that these ships will deliver to the UK armed forces for the next 20 years and beyond.”

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