Marilyn More said Tuesday staff within her department concluded that the integrity of the MV Miner's hull is in question.
"There started to be questions among our staff about whether or not we could ensure that would be a safe workplace for workers," she said after a cabinet meeting.
Provincial officials issued a verbal stop-work order Friday and followed up with a written order Monday.
The weather in the area off Scatarie Island where the ship is stranded is getting worse, raising more questions about worker safety, More said.
"The deterioration was progressing ... It was potentially increasing the risk to workers at that site."
More said the salvage company, the Bennington Group of New York, has agreed to hire an independent engineer to assess the site and review the company's safety practices.
The department says work to dismantle the 230-metre vessel will not begin until the assessment is complete.
The retired Great Lakes bulk carrier ran aground off Cape Breton more than a year ago. It was being towed to Turkey to be scrapped, but its tow line broke in heavy seas.
The salvage project has been delayed several times since the province gave approval for the Bennington Group to remove the ship in the spring.