However, he said the final decision rests with the MoD if a yes vote would affect the location of where the ships are built.
Ian King CEO of BAE Systems, replied to Ian Davidson, Glasgow South West MP and chair of the Scottish Affairs Committee at Westminster who wrote following the reports in the Evening Times last week that the firm was planning a £200m frigate factory at Scotstoun with the possibility of retaining Govan shipyard regarded as "sub-optimal".
Mr King said: "We have agreed with MoD that we would work on our current plan.
"We are not working on any alternative, or contingency plan to the one agreed with MoD and nor have we been asked to by the department.
"It is for the Scottish people to determine the outcome of this year's referendum on independence.
"In the event of a yes vote and as we have made clear, we would be required to discuss the future of the type 26 programme with our customer, the MoD.
It would be for the MoD to determine how the vote affects the final decisions they have yet to make on the programme, including the future location of the build of the ships."
Mr Davidson said the future of shipbuilding on the Clyde is uncertain if Scotland votes for independence.
He said: "This shows clearly that, as we have previously stated, the only guarantee for the future of shipbuilding on the Clyde is for Scotland to remain part of the United Kingdom."
The SNP has said the Clyde was chosen because it is the best option for BAE and the UK government to build the ships.