The aircraft carriers being built for the Royal Navy will be less useful, take longer to finish, and likely cost more than claimed, a parliamentary watchdog warns.

The first, HMS Queen Elizabeth, will be mothballed immediately it is launched in 2016, according to the existing plan. However, the second, HMS Prince of Wales, is not now expected to be fully operational until 2031. Moreover, it will only be able to stay at sea for up to 200 days a year, significantly fewer than envisaged, says the Commons public accounts committee.

The MPs' report, out on Tuesday, makes clear the quick decision to adapt the carriers to fly US-made Joint Strike Fighters, taking off by catapult and landing by arrester wires, will increase the planes' cost as well as that of the carriers, but by how much will not be known until December 2012.

The cost of the US JSFs – or F35s as they are now called – is spiralling, and the Ministry of Defence has already cut substantially the number it plans to buy; development is also threatened by pressures on the American defence budget.

The catapult/arrester arrangement enables British aircraft to land on French carriers, and vice versa – increasing co-operation; the UK version also has longer range and carries heavier weapons.

The report says that the construction of the carriers themselves is "progressing well", but warns the costs of converting the carriers "are not yet fully understood".

It continues: "The technology proposed has yet to be tested and the [fighter] version the UK intends to buy will be unique to Britain. The costs of converting the carrier for use with the carrier variant aircraft will not be known until 2012."

Margaret Hodge, the former Labour minister and chair of the public accounts committee, told the Guardian: "The carriers' starting cost was £3.5bn, is currently about £6.2bn, and is likely to rise to up to £12bn. There will be nine years without a carrier, and it will be at sea for fewer than 200 days on average."

She accused David Cameron of deceiving parliament by claiming, after the defence review was agreed last year, that cancelling the carriers would have cost more in compensation to BAE Systems, the builders, than going ahead with them. According to the MoD's own figures, cancelling both ships would have immediately cost the government £2.4bn in cancllation fees but would have led to savings of £1.2bn in the long term.

Cancelling one ship, but going ahead with the other, would have saved just £200m in the long term.

Jim Murphy, the shadow defence secretary, said: "Yet again we have a respected body giving a damning assessment of the defence review, which was driven by short-term cash savings, not strategic need, and limits Britain's ability to project power".

He added: "It will worry those in the services that ministers' projected savings are in fact deferred expenditure, and so the long-term impact of their policy decisions on the defence budget and equipment programme remains unknown."

Murphy also raised questions about the government's decision, announced on Monday, to sell to the private sector the existing Royal Navy and RAF search and rescue service from 2015. There are 91 navy and RAF search and rescue pilots, including Prince William. "That would be a further blow to falling morale in the services as well as a waste of their valuable skills," Murphy said.

An MoD spokesperson said: "It is incorrect to claim that a full carrier strike capability will not be achieved until 2030. The more capable carrier variant of the Joint Strike Fighter fast jet will begin operating from our aircraft carrier from 2020, with six UK jets available for operations.

"By 2023, this number will increase to 12 UK jets onboard and we will be able to work with our allies to increase that number".

The defence secretary, Philip Hammond, said: "When this government came into power, [the carriers] were already £1.6bn over budget ... Until our new carrier capability comes into service, we can utilise our extensive basing and overflight rights to project decisive air power, as we showed during the Libya campaign."