The biggest ever warships built to protect British interests will be completed in Scotland even if there is a Yes vote for independence, in another blow to the “Better together” campaign.

Ministry of Defence officials and industry leaders have previously warned that thousands of defence jobs would be lost in Scotland post-secession, as work related to national security would have to be kept within redrawn national borders.

One of the most obvious losses was thought to be the second of two aircraft carriers worth £6.2bn that are being assembled in Rosyth. They are vital to the future of the Armed Forces, as each has 40 jets and helicopters capable of 108 sorties a day.

Download the new Independent Premium app Sharing the full story, not just the headlines

HMS Prince of Wales carrier starts being pieced together at the Rosyth dockyard, using parts built across the UK, in September. The first carrier, HMS Queen Elizabeth, is being assembled in Rosyth but will not formally become part of the Royal Navy until 2017. HMS Prince of Wales is not fully operational until 2022 – six years after Scotland might have become a separate state. However, a senior naval source said that the carriers have “got to be finished” at Rosyth, ensuring 2,000 jobs for years to come.

Angus Robertson, the SNP’s leader in Westminster and defence spokesman, said: “These are welcome comments, and put to bed the scaremongering from the No campaign about Rosyth.”

However, Alistair Carmichael, the Secretary of State for Scotland, said that he would check the terms of the aircraft carrier contracts. He added: “That work will not last for ever. When that’s finished, what will they [Rosyth dockyards] do then?”