Gordon Matheson was speaking after it was revealed yard operator BAE Systems was considering investing in a giant "frigate factory" at Scotstoun, spelling the end of shipbuilding in Govan.
BAE Systems has made no final decision on the shape of its facilities in Glasgow if, as expected, it wins a contract to build a new generation of Type 26 frigates for the Royal Navy.
An announcement is expected next year but the company has two options: build the ships in both yards or invest heavily in a single state-of-the-art yard at Scotstoun.
It has entered in to informal talks with the city council on expanding the facility on the north bank at Scotstoun.
Mr Matheson, in a carefully worded statement, said: "It is clear that the frigate order secures the long-term future of shipbuilding on the Clyde.
"The MoD contracts protect apprenticeships and highly-skilled jobs, and will also deliver massive investment.
"And while no decisions have yet been made, it is crucial that BAE maintains an open dialogue with the workforce about the best way of delivering this contract.
"I will continue to take my steer from the trade union leadership in the yards, and, alongside the unions, will work closely with management to protect jobs and develop Clyde shipbuilding for decades to come."
BAE Systems on Thursday and yesterday continued to brief its workforce on the two options. It is also looking at down-scaling operations from its current work building two giant aircraft carriers for the Royal Navy.
Last month the company announced more than 1700 job losses over the next three years, 800 in Scotland, with most of the rest in Portsmouth, where the BAE yard will stop building ships.
It is understood BAE Systems will need the same number of workers whether it operates over two yards in Glasgow or one.
The Govan yard, the old Fairfields, is owned by infrastructure giant Clydeport rather than BAE Systems.
It recently began preparations to dismantle its cranes, the last of their kind on the Clyde. Management insist the cranes, unused for five years, are outdated. However, sources describe them as serviceable.
The Govan yard, even if it shuts, would not do so until at least 2017.
BAE is currently negotiating with the UK Government to build a new generation of frigates, called global combat ships or Type 26s, for the Royal Navy.
It is expected to put detailed proposals for this work, including exactly where they will be built, to the Ministry of Defence next year.