The defence giant has two yards on the Clyde and is currently looking at plans for a single new multi-million-pound frigate factory at Scotstoun.
The firm does not expect to secure a major contract for a new generation of Type 26 global combat ships until after September's big vote.
But chief executive Ian King has admitted England has no yards capable of making such ships.
Mr King said BAE had "no contingency plans" to deal with a yards vote and all of the company's capability for building complex warships exists north of the Border.
He added: "If Scotland becomes independent…then we will have to have a discussion with our customer, the Westminster Government, about how they would like to deal with that," he said.
Angus Robertson MP, SNP Westminster Leader and Defence spokesperson said: "These comments make clear BAE's firm commitment to production in Scots yards in an independent Scotland.
"This sensible intervention is very welcome indeed - and completely demolishes No campaign scaremongering on shipbuilding jobs."
Industry insiders have long argued the Clyde is the only option for building the frigates, whatever the outcome of the referendum because moving production south would be hugely costly for BAE.
John Robertson, the Labour MP for Anniesland, said: "The Type 26 contracts will not be awarded until the referendum has taken place. Is that a coincidence? I don't think so."