The union representing crews on Clearwater Seafoods factory freezer trawlers says it was unaware of health concerns that prompted authorities to shut down automatic scallop shucking machines on three vessels.

Nova Scotia's Department of Labour ordered the machines shut down Friday, after crew members complained airborne particles were causing nose bleeds, bloody coughs and headaches. Crewmen told the province's Department of Labour the machines on board Atlantic Protector and Atlantic Guardian made them sick.

"It only became prevalent once the shucking machines were on board and operational. That led us to believe there may be a problem," said Gregory Green, the acting director of investigations for the Department of Labour.

He said saws on the machines generate a fine dust, which mixes with water creating "a visible cloud in the work space."

There is a further concern that contaminants are vented into crew living spaces.

"I received an email Saturday afternoon of the work-stop order," said Blair Benjamin, of the United Food and Commercial Workers Union.

"That came from the HR department of Clearwater. I was just as surprised as they were in terms of seeing what was in the report."

Stop-work orders issued Friday

On Friday, Nova Scotia's Occupational Health and Safety division issued stop-work orders to Clearwater Seafoods, shutting down automatic shucking machines developed by the company and installed last year.

Clearwater Seafoods scallops. (CBC)

"I haven't received any calls over nose bleeds, spitting up blood even from the standpoint of any claims that have gone through to the workers compensation board," Benjamin told CBC News.

The company has until Nov. 5 to improve the exhaust system and develop a respiratory protection program for the crew. It has until Nov. 19 to take air quality samples while all the machines are operating.

The order directly affects about 80 crew members on board Clearwater's two active Shelburne-based trawlers: the Atlantic Guardian and Atlantic Protector. Both are at sea, where crews are now shucking scallops by hand.

Benjamin said the vessels are expected back in port on the weekend so the company can deal with the issue.

"They are going to address the problem as soon as possible. They are in the mix now working on the ventilation and all of that stuff. It will be done as soon as the vessels hit the shore," he said.

Benjamin said for now, crew members stand to lose bonus money because of the forced return to hand shucking scallops.

Christine Penney, the vice-president of sustainability and public affairs for Clearwater Seafoods, told CBC News the company was unaware of crew health concerns but will comply with the orders.

"We do believe we can install ventilation around this equipment that will meet the OHS requirements," she said.

"We've immediately ceased the operation of this equipment to re-evaluate and address the concerns that OHS has raised."

The company is being praised for its response.

"Clearwater has been very co-operative. They are very concerned about the issue themselves and are taking our order seriously," said Green.

Set back for a technological breakthrough

Automatic shucking machines were introduced on the Atlantic Guardian and Atlantic Protector vessels in 2011.

The company developed the technology itself. According to the Clearwater website it "replaces the manual method of shucking scallops by making use of several different mechanical processes combined in a relatively compact piece of equipment that withstands the rigors of offshore fishing."

Last November, the federal government's National Research Council and the Canadian Manufacturers and Exporters Association recognized the technology.

"It's innovative technology. It has impacted the productivity of the vessels and it's assisted the health and safety of our workers. It's actually more ergonomically friendly than the previous method of shucking scallops," said Penney.

She said independent air emission tests, carried out before and after the machines were installed, met guidelines.

The province said the sampling method should have taken into account the actual concentration levels faced by crews.