The defence giant insists it has made no final decision on the future of its two sites in Glasgow - just two months after announcing more than 1700 job losses, including about 800 in Scotland, as it winds down from its current aircraft carrier orders.
It has been widely rumoured the company will focus its energies on building a new generation of frigates at a single yard in Scotstoun, shutting the historic Fairfields site at Govan.
However, there is also understood to be a less favoured plan to build the new vessels, Type 26s or Global Combat Ships, across two sites, keeping both Govan and Scotstoun open.
BAE Systems has now formally notified Glasgow City Council of planning proposals for both options. It had to do so because the sheer scale of the works envisaged is so big that it has a duty to enter into a statutory pre-planning application consultation with stakeholders such as community groups.
A letter from consultants Arch Henderson, acting for BAE Systems Naval Ships, told Glasgow City Council it would submit a planning application for "new buildings, new site access and associated works" at the Scotstoun yard in South Street.
It added: "The proposed development is one of a number of options that BAE are currently evaluating with the regard to their shipbuilding and support operations."
The consultants stressed the plan was a "major development" and BAE was therefore committed to a "full and frank community consultation".
An almost identically worded letter was written to the council for "new buildings and associated works" at Govan.
Gordon Matheson, the leader of Glasgow City Council, has already signalled he would accept the closure of Govan if such a move had union support.
BAE is understood to have briefed senior politicians in Scotland about its proposals.
Despite the historic status of Fairfields, most industry insiders believe focusing investment at a single new state-of-the-art yard would be a signal of long-term confidence in Clyde shipbuilding. Such a move could potentially free up space at Govan for another use.
It is understood BAE will need the same number of workers whether it operates from one or two yards.
BAE began to explain its decision-making process to workers last month. At the time, a company spokeswoman said: "We are undertaking initial exploratory work to assess potential options to invest in these manufacturing facilities.
"No decisions have been made and the discussions are part of our ongoing consultation with our employees and trade unions. Our aim is to create a world-class warship design, build and integration capability, ensuring that we deliver value for money to the Ministry of Defence and a modern and safe workplace for staff."
BAE is currently negotiating with the UK Government to build a new generation of Type 26 frigates for the Royal Navy.
It is expected to put proposals for this work, including exactly where they will be built, to the Ministry of Defence next year.
Even if a decision was made to close the Govan yard, it would stay open until at least 2017 as it completes work on two aircraft carriers and an order for offshore patrol vessels.
BAE Systems announced the closure of its third surface ship yard, in Portsmouth, late last year.
The English yard, which is a decade old, was widely expected to be axed.