The company, which employs thousands of people north of the border, made the statement in its annual report.
BAE Systems joins a list of firms including Standard Life, Royal Bank of Scotland, Shell, Lloyds and Barclays in highlighting the risks associated with the September vote.
Its report says: "The decision on independence is a matter for the people of Scotland.
"However, BAE Systems has significant interests and employees in Scotland, and it is clear that continued union offers greater certainty and stability for our business.
"In the event that Scotland voted to become independent, we would need to discuss the way forward with the Ministry of Defence and UK Government, and work with them to deliver the best solution in those circumstances."
BAE Systems has a number of defence contracts with the UK Government, including warship building at the Scotstoun and Govan yards on the Clyde.
A Better Together spokesman: "This is an important intervention from one of Scotland's largest employers and underlines the huge risks involved with leaving the UK.
"The defence industry employs thousands of people in Scotland because we are part of the UK. If we walk away from the UK then we walk away from the UK investment that sustains the jobs of so many communities throughout Scotland."
A spokesman for Scotland's Deputy First Minister, Nicola Sturgeon, said: "The simple fact is that 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."