"The men and women who work on the Eurofighter are highly skilled and the potential loss of these jobs would have an appalling impact on them, the local economy and wider supply chains".
Chief executive Charles Woodburn said: "The organisational changes we are announcing today accelerate our evolution to a more streamlined, de-layered organisation, with a sharper competitive edge and a renewed focus on technology".
She said the cuts were the result of internal restructuring, and "not related to any United Kingdom defense spending decisions".
BAE is also making 12 Typhoon jets for Gulf state Oman.
The report comes amid a slowdown in demand for Eurofighter Typhoon fighter jets, which are assembled at the Warton and Samlesbury plants.
As a Saudi follow-on order for Typhoon fighter jets failed to materialise this year, a Qatariorder for these jets and Hawk trainer airplanes may provide a lifeline for troubled British defence company BAE Systems.
Jobs will also be cut at Brough in East Yorkshire and at RAF bases in Marham, Norfolk, and Leeming in North Yorkshire.
The company is reportedly considering the elimination of some 2,000 jobs at United Kingdom plants that make the Eurofighter Typhoon amid declining orders for the aircraft.
Unite vowed to fight what it called a "devastatingly short-sighted decision", claiming job losses would undermine Britain's sovereign defence capability and devastate communities.
More jobs will go from the company's cyber intelligence business in London and Guildford. Around 375 job losses are planned for the maritime servicing and support business, with 340 in Portsmouth.
Defence analyst Howard Wheeldon said the cuts were essentially due to a gap in orders emerging in key programmes. "It takes out a management layer and lays out a new structure and the people for the years ahead".
The company said on Tuesday that discussions with current and prospective operators of the Typhoon continued to support its expectations for future contract awards.