The NAO queried whether the changes represent value for money and pointed out there would be a decade-long gap without aircraft carrier capability.
Margaret Hodge, chairman of the Commons Public Accounts Committee, said the report was "deeply worrying".
Defence Secretary Liam Fox said changes put the programme "back on track".
In its report, the NAO said changes to the carrier programme in the government's strategic defence and security review (SDSR) had created "significant levels of operational, technical, cost and schedule uncertainty", with the final total cost of the programme now set to exceed ?10bn.
The ships - HMS Queen Elizabeth and HMS Prince of Wales - were saved from defence cuts under the coalition government because it said it would cost more to cancel the projects than proceed with them.
Ministers agreed to change the design of one, or both, of the aircraft carriers to make them compatible with the US Navy's version of the Joint Strike Fighter.
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Caroline Wyatt Defence correspondent, BBC News The NAO's worries are that the impact of the changes is not yet fully understood by the MoD.
Such a major project requires a huge amount of planning and technical preparation, and costs have already escalated significantly since the project began. The government's decision to change the variant of the aircraft to go on board - from the short-take off and vertical landing version of the joint strike fighter to the carrier version that requires catapult and arrestor gear - has added new risks to the project, which range from financial to operational.
While the decision to buy the more capable version of the aircraft makes operational sense, as it can drop heavier weapons and has a greater range, the 'cats and traps' that will be needed for take-off and landing are a whole new system which hasn't yet been trialled or used.
Regenerating the Royal Navy's ability to launch aircraft from a carrier after a gap of 10 years will bring its own challenges, in ensuring crews are trained, ready and able to perform this intricate and demanding job.
The report also makes clear even under the previous government's plans, the MoD had a "funding gap" when it originally ordered the carriers - the order went ahead on the basis the MoD would make other savings in order to be able to afford the carriers.
The NAO said the way the SDSR was conducted was "not the ideal situation in which to have to take strategic decisions", and it has warned it is concerned the carrier programme may be vulnerable to further changes if the promised increases in defence spending don't materialise in 2015.
HMS Prince of Wales will not enter service - it will be built but not kitted out, and then kept as a reserve vessel - while HMS Queen Elizabeth is expected to go into service around 2020, with both said to cost some ?6bn.The NAO said the decision to buy a different version of the aircraft has delayed the entry into service date by two years, leaving the UK without a carrier able to launch aircraft for a decade and adding significant new risks to the project.
The Whitehall spending watchdog pointed out the decision to make only one carrier with aircraft operational means the UK will only have a carrier at sea for between 150 and 200 days per year - meaning it will rely heavily on allies to fill the gap.
Ms Hodge said the report also revealed that cancellation of the aircraft carriers had been feasible.
She said the report showed cancelling one carrier would save ?200m in the long term and cancelling both would save ?1.2bn over the same period.
Ms Hodge told the BBC: "It's a very depressing report. This is a project that has been plagued with poor decision-making.
"What the government decided to do in the defence review was substantially change the design and buy a different plane.
"What the report says is that it's something technically which has never been achieved elsewhere in the world and that we have no idea of the costs.
"What we are getting is a delay without a capability for a decade of a carrier on the seas.
"The costs haven't been cut, they've been delayed by delaying the purchase of the plane, by mothballing one of the carriers."
But BBC defence correspondent Caroline Wyatt said the MoD's own list of options contained in the report showed that would have meant accepting the demise of the UK's shipbuilding industry.
Dr Fox insisted that decisions made in the defence review had cut the overall costs by more than ?3bn.
He said: "We inherited a complete mess from Labour, a carrier programme which they didn't have the money for in the budget, where they had the wrong design on the ship, and the wrong planes to go on it.
"So we inherited a starting point that we would not have chosen, but having said that, we had to take the appropriate decisions to make it inter-operable with the United States and to give us 50 years of the best utility we could have in terms of power projection."
Last November, the UK and France signed a defence treaty that agreed to share aircraft carrier resources by keeping at least one vessel at sea between the two countries at any one time.
Each will be able to use the other's carrier in some form for training and possibly for operations.
The SDSR in October 2010 outlined cuts of ?4.7bn over four years.
The new carriers will replace the 22,000-tonne Invincible class aircraft carriers, HMS Invincible, HMS Illustrious and HMS Ark Royal.
HMS Invincible, mothballed in 2005, was put up for sale on a government internet auction website, while Ark Royal - the navy's flagship - was decommissioned in January and HMS Illustrious will be decommissioned in 2014.
Displacement: 65,000 tonnesLength: 280m (920ft)Width (at flight-deck level): 70m (230ft)Keel to masthead: 56m (184ft)Nine decks (plus flight deck)Speed: 25+ knotsRange: 8,000-10,000 milesAircraft: 36 F-35 Joint Strike Fighters and four Airborne Early Warning aircraft, plus EH 101 Merlin helicoptersCrew: 1,450 (including air crew)Weapons: Phalanx close-in weapon systems; 30mm and mini-gunsSource: Ministry of Defence
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