In its annual report the company said a No vote offered "greater certainty and stability" for its business.
BAE, which employs thousands of people in Scotland, joins a list of firms, including Standard Life, Royal Bank Of Scotland, Shell, Lloyds and Barclays, that have highlighted the risks associated with the September vote in recent weeks.
A Better Together spokesman said the comments were an "important intervention from one of Scotland's largest employers".
He added: "Alex Salmond may think thousands of shipyard jobs are a price worth paying to achieve his lifelong dream of independence, but most people in Scotland don't agree."
A spokesman for Deputy First Minister Nicola Sturgeon dismissed the comments, saying the "simple fact is the Clyde, with its hi-tech yards and world-class workforce, is the only credible place in these islands with the capacity to build these ships."
The spokesman added: "Defence companies are used to working within changing international parameters, and will continue to do so within an independent Scotland."
Shadow Scottish Secretary Margaret Curran said: "It is time the SNP came clean with people across Scotland and admitted their plans for shipbuilding do not add up."