The company, which employs thousands of people north of the border, made the statement in its annual report published today.
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 states: "In September 2014, Scotland will hold an independence referendum.
"The decision on independence from the UK 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 on the Clyde.
Responding to the company's annual report, 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."
He added: "The UK Government has never built a warship outside of the UK. The idea that we could leave the UK but UK warships would continue to be built here simply isn't credible.
"Alex Salmond may think that thousands of shipyard jobs are a price worth paying to achieve his life long dream of independence, but most people in Scotland don't agree."
Labour's shadow Scottish secretary Margaret Curran said: "Thousands of jobs in Scotland rely on shipbuilding. Not just in our yards but also in the vast supply chain that supports jobs in businesses across the country.
"It's time that the SNP came clean with people across Scotland and admitted that their plans for shipbuilding just don't add up."
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.
"Scotland's shipyards have the expertise to secure UK and worldwide orders - and following independence there will also be orders for the Scottish Defence Force.
"Scottish companies will also be able to bid for any MoD contracts that are put out to competitive tender. The MoD places contracts with companies in Korea - so there is no reason that it could not do so with companies in Scotland.
"Defence companies are used to working within changing international parameters, and will continue to do so within an independent Scotland."