Delays in committing funds and ordering the Royal Navy's two new aircraft carriers could leave the fleet with a "damaging capability gap" and affect medium-term employment in yards on the Clyde and elsewhere, the Commons Defence Committee will warn today.

With negotiations between the Ministry of Defence and shipbuilders still bogged down in cost and industrial restructuring arguments, the 60,000-tonne warships will not make their in-service deadline around 2013 unless decision are taken soon. This would have implications for the defence of the UK and its sea-lanes, and military operations globally. It would have an impact also on commercial shipyards throughout Britain.

The committee will also express concern over how much of the secret technology promised by the US for the 150 Joint Strike Fighters - the basis of the Navy's carrier strike force - will be delivered.

The MoD has refused to show committee members a set of confidential assurances offered by Washington that the UK will have complete autonomy over the stealth jets' computer programmes. Whitehall threatened to cancel its £10bn order for the JSFs last year because of US reluctance to share technology it feared might leak to potential future opponents such as China.

While welcoming the launch of the defence industrial strategy, an MoD initiative to persuade the UK shipbuilding sector to consolidate and rationalise, the committee said it would only succeed if companies were confident future orders would be placed and not delayed or scrapped, and adequate funding was ring-fenced for naval construction.

The MoD has already slashed its planned order for Type 45 destroyers from 12 to six and is still considering whether to order a fourth Astute nuclear hunter-killer submarine. The Government has not confirmed that an order for two other Type 45s to be built at BAe's Clyde yards has already been shelved.

James Arbuthnot, the Defence Committee chairman, said last night: "In many areas, the MoD has done well in implementing the defence industrial strategy, but there remains a lot to be done."