It also revealed a £1.3billion cut in sales as a result of major cutbacks in defence spending around the world.
But Britain's biggest defence contractor still declared a pre-tax profit for 2012 of £1.89bn and global sales of £17.83bn as well as a backlog of orders worth a staggering £42.4bn.
BAE Systems, which is one of the world's largest defence companies, is "well positioned" for the future, according to chief executive Ian King, who added: "BAE Systems continues to deliver a robust performance with strong trading in a number of areas."
Key activities across Scotland, including the shipyards at Scotstoun and Govan, as well as an aviation repair and maintenance centre at Prestwick, South Ayrshire, were highlighted.
They included the Clyde-built Type 45 fleet with the hand over last year to the Royal Navy of the fifth destroyer HMS Defender and successful sea trials of the sixth and last in fleet HMS Duncan which is due to leave Glasgow in a few weeks.
Other highlights were the construction and delivery of the largest ever block built for the new super sized aircraft carrier HMS Queen Elizabeth and the start of work on a block for a second carrier HMS Prince of Wales.
Mick Ord, managing director of BAE's maritime and naval ships division, said: "The last 12 months have once again showcased the fantastic skills and capabilities within BAE Systems in Scotland.
"We've delivered all of the major hull sections of the first Queen Elizabeth aircraft carrier to Rosyth, where the ship is taking shape in the dry dock and construction on the Prince of Wales is well advanced across our yards."