The defence giant, which currently employs 3000 staff in Scotland, is currently operating at peak capacity owing to work on the Queen Elizabeth and Prince of Wales aircraft carriers, with work taking place on different sections in Govan and Scotstoun in Glasgow.
The carriers are being assembled at Babcock's site in Rosyth.
The first carrier in the class is due to be handed over to the Royal Navy in 2016, while work on the second is now taking place at BAE yards around the UK.
A spokeswoman for BAE said talks are now taking place with the MoD over the level of shipbuilding capacity the firm will ultimately require in the UK after the carrier contract is complete.
BAE is currently working in partnership with the MoD on the assessment stage of plans to build the new Type 26 frigate, a class of 13 new anti-submarine warships to replace the Type 23.
A decision by the MoD on which yards will ultimately carry out the work is not understood to be imminent, but the spokeswoman said its work on the assessment process was gathering pace.
She noted BAE had announced its first design partners for major equipment for the ships last month, and confirmed manufacturing is due to start in 2016, with the first entering service "as soon as possible" after 2020.
The spokeswoman said the talks with the MoD are "focused on developing a managed transition from this peak to the long-term steady state required to deliver the Type 26 programme".
BAE gave the update on its naval arm in an interim management statement for the period covering July 1 to October 9.
It said trading has been consistent with the management expectations signalled when it announced its half-year results on August 1, noting its outlook for the full-year remains unchanged.
The company said: "In aggregate, including both the benefit from the share repurchase programme and downside arising from reductions to US defence budgets, double-digit growth in underlying earnings per share is anticipated for 2013."
Beyond its UK naval business, BAE said it was confident of a positive outcome to talks with the Saudi government over the "price escalation" of Salam Typhoons, but said if talks dragged into next year it could impact on earnings per share by 6p to 7p.
It has lodged a bid to supply Typhoon aircraft to the United Arab Emirates, and said it had taken orders worth £5 billion from outside the UK and US this year.
In the US, the group noted the impact of "budget uncertainty" and potential effects of the federal shutdown, sparked by Congress' failure to agree a spending bill.
BAE said: "Whilst the impact of this action has not yet been material to the group's financial performance, some progressive impact to the group's US operations would result from a protracted government shutdown.
"Since the October 1 shutdown, approximately 1200 employees across the intelligence and security and support solutions businesses have been temporarily directed not to work."
The company reported that in August it had won an eight-year, £331 million contract to maintain the Minuteman III intercontinental ballistic missiles in the US.
Shares in BAE closed up 10.70p at 450.7p.