Britain's troubled and increasingly expensive plan to equip the navy with new aircraft carriers has been plunged into fresh turmoil as ministers consider reversing their earlier decision to change the type of plane that should fly from them, it has emerged.

The government announced in last autumn's strategic defence review that it had decided to buy the "cats and traps" (catapults and arrester gear) version of the US joint strike fighter. This would have a "longer range and greater payload ... the critical requirement for precision-strike operations in the future", the government stated.

Moreover, the government added, it will be cheaper. It would also enable French planes to land on British carriers, and vice versa, inkeeping with the new UK-French defence spirit of co-operation.

Now, in an extraordinary volte-face, the Ministry of Defence says the "cats and traps" planes may well be cheaper but it would be too expensive to redesign a carrier – more than £1bn – to accommodate them. The ministry is thus faced with the prospect of renegotiating a deal with the US, reverting to its original plan – namely buying the short take-off and vertical landing version of the aircraft, even though it is acknowledged to be less effective and more expensive .

The latest chapter in the troubled saga of Britain's future aircraft carriers – whose own estimated costs have soared – was raised on Thursday in a letter to the defence secretary, Philip Hammond, from Jim Murphy, his Labour opposite number.

Murphy referred to "worrying suggestions" that the government was about to change its mind about the kind of aircraft to buy from the US. "It is vital that there is now clarity on the government's plans for this vital area of the defence equipment programme," he wrote.

Murphy said the decision in the defence review to scrap the Harrier fleet meant the UK would have no carrier aircraft capability until 2020 – and then only one carrier would be operational.

Defence officials said that the government was "re-assessing" its earlier decision because, they indicated, of pressures on the defence budget.

HMS Queen Elizabeth, the first carrier, will be mothballed immediately it is launched in 2016, according to existing plans. The second, HMS Prince of Wales, will be able to put to sea by 2020, but it is not known how many planes will be able to fly from it – nor what kind.

The two carriers, originally priced at £3.5bn, are now estimated to cost £6.2bn. According to the Commons public accounts committee, the cost is likely to icrease to as much as £12bn.

The government, which originally said it wanted more than 100 joint strike fighters, says that it will have just six operational ones by 2020. The unit cost of the joint strike fighter, made by Lockheed Martin, has soared because of production problems and delays caused by US defence budget cuts. Britain's BAE Systems and Rolls-Royce have big stakes in a future deal adapting the joint strike fighter for British forces.

A spokesperson for the MoD said: "We are currently finalising the 2012-13 budget and balancing the equipment plan. As part of this process, we are reviewing all programmes, including elements of the carrier strike programme, to validate costs and ensure risks are properly managed. The defence secretary expects to announce the outcome of this process to parliament before Easter."

• This article was amended on 5 March 2012 because the original referred to "cats and traps" as "cats and flaps". This has been corrected.