Several hundred employees have staged a walkout at the Rosyth industrial complex on the Firth of Forth, according to trades unions.
Unions say that they are going to organise a postal ballot
A union official said the protest was "workforce-led" and followed a mass meeting about planned changes in pension arrangements.
The site, which includes the former Rosyth Royal dockyard, is operated by Babcock Engineering Services.
A spokeswoman for the company declined to comment.
Workers at Rosyth are expected to return to their jobs on Thursday, but the unions involved are to organise a postal ballot on invoking formal sanctions.
The unions claim the company suddenly ended talks on the pension issue and announced that the changes would be imposed from 1 July.
John Park, a former Rosyth dockyard worker and new MSP for Mid Scotland and Fife, has called on Babcock management not to impose the pension deal.
Mr Park said he had written to the firm asking it to reconsider the plans.
He said: "I've urged them to get back to the negotiating table and not to forget the importance of stable industrial relations for their future success."