Admiral Lord Alan West said the government is trying to purchase a different variant of the state-of-the-art F-35 which is unable to land on decks of the Queen Elizabeth-class carriers.
The Labour peer claimed some within Whitehall were keen on purchasing the F-35A over the currently-agreed F-35B jets, which are capable of hovering and landing vertically, like Britain's former fleet of Harrier jump jets used to.
The F-35A variant of the sophisticated stealth jet does not have that ability. This, combined with the fact the carriers don't have the equipment to allow the jets that can't set down vertically to land, means they could never operate from the warshipsÂ '“ worth a combined Â£6.2bn.
Former First Sea Lord, Lord West said if this happened it would dull the potency of Britain's future carrier strike battle groups, by limiting the total number of jets able to operate from the aircraft carriers during a war.
Speaking to The News, he said: '˜There's no doubt there's a lobby in the Royal Air Force who don't really like carriers and want to go for the F-35A.
'˜They say this is a cheaper option and that the F-35As have longer legs and a better range than the F-35B. What they fail to realise is a squadron of F-35Bs on a carrier can move 500 miles a day closer to the enemy.
'˜I am very concerned that if they start going down this route then it infringes on the carriers' capabilities.
'˜The whole point of going for the F-35B is because it works with the carriers.
'˜It's clearly completely bonkers to order an airplane that can't fly on and off the carriers. It contradicts the whole idea of carrier strike.
'˜The MoD is trying to do this by stealth which is completely unacceptable.'
Britain plans to buy at least 138 of the jets. which are the most advanced in the world, in a project the government claimed could be worth Â£35bn to the UK economy.
The jets cost Â£92m each to build, although the MoD expects this cost will shrink as time goes on and development costs reduce.
Currently the government is working on purchasing the first batch of 48 F-35B jets.
When questioned in the House of Lords, defence minister Earl Howe said the ModÂ was '˜on track' to deliver the first traunch of F-35Bs.
However, he stopped short of guaranteeing all of Britain's new jets would be of the same model, saying the decision on future purchases would be '˜taken at the appropriate time'.
Responding to Lord West's concerns, Earl Howe said: '˜The first tranche of 48 aircraft will be the F35B, which is capable, as the noble lord knows, of operating from land and the Queen Elizabeth-class aircraft carriers.
'˜Decisions on subsequent tranches of [F-35] Lightning will be taken at the appropriate time.
'˜Of course, the number of aircraft deployed will depend on the circumstances and the nature of the deployment.
'˜The minimum number to be deployed will be one squadron; that is, 12 aircraft. The plan is for full operating capability in 2023, with two squadrons, but of course there is scope for each carrier to have as many as 36 aircraft deployed on it.'
Earl Howe said the MoD was '˜on track and within budget' to deliver both jets and pilots and said one squadron on the carriers would consist of '˜12 frontline F-35s and 18 pilots' in December 2020.
'˜Full operating capability, consisting of two squadrons, will be achieved in December 2023,' he added.