The Department of Labour and Advanced Education said the order requires New York-based Bennington Group to hire an independent engineer to complete an assessment on the structural integrity of the MV Miner.
Pat Murphy of the department's occupational health and safety division said the engineer will assess the ship's hull and determine whether it is safe for workers.
"We're now into the fall and winter season in Atlantic Canada, weather and additional stress and force has been applied to the hull of this vessel, which was already compromised because of the grounding," Murphy said from Sydney, N.S., on Sunday.
"Our primary concern has to be that the people who go out to do this work come home safely at the end of the day."
Murphy said the engineer will also review the procedure that the company will use to dismantle the vessel, which ran aground off Scatarie Island on Sept. 20, 2011, while being towed to a scrap yard in Turkey.
He said the department met with Bennington Group officials over the weekend, who said they would comply with the order.
"They were very co-operative ... and assured us that they're anxious to get this project completed."
The Bennington Group could not be reached for comment on Sunday.
The department says work to dismantle the 230-metre bulk carrier will not begin until the assessment is complete.
The project has been delayed several times since the province gave approval for the Bennington Group to remove the ship in the spring.
Earlier this month, the project was put on hold after three new plasma cutters and some robotics equipment were stolen from a work site at the Sydport Industrial Park in Sydney.
In September, the company was given another three months to complete the work. Under the provincial permit, the company has until Dec. 1 to remove the derelict ship. The original deadline expired Aug. 31.
Some preparation work has been done — such as building barges to transport heavy equipment — but little to no work has been completed at the actual site, said Murphy.
Murphy said he could not comment on whether the stop work order would affect the Dec. 1 deadline.