Gordon Matheson was speaking after the Evening Times revealed yard operator BAE Systems was considering investing in a giant "frigate factory" at Scotstoun, spelling the historic end of shipbuilding in Govan.
BAE Systems has made no final decision on the shape of its Glasgow facilities if, as expected, it wins a contract to build new generation Type 26 frigates for the Royal Navy.
The company is expected to make an announcement next year but has two options: build the ships across both yards or invest massively in a single state-of-the-art facility at Scotstoun.
It has entered into informal talks with Glasgow City Council on the expansion of the yard on the north bank.
Mr Matheson said: "The frigate order secures the long-term future of shipbuilding on the Clyde. The MOD contracts protect apprenticeships and highly-skilled jobs, and will 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 yesterday continued to brief its workforce on the two options. It is also looking at ways to downscale operations from its current work building two aircraft carriers for the Royal Navy.
Last month the company announced more than 1700 job losses over the next three years. Some 800 of those posts will go in Scotland with most of the rest in Portsmouth, where its yard will go back to its previous work repairing rather than building ships.
It is understood BAE Systems will need the same number of workers whether it has 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. Bosses insist the cranes, which haven't been used for five years, are outdated. However, sources describe them as serviceable.
The Govan yard, if it was to shut, would not do so until at least 2017.