HALIFAX -- A Nova Scotia judge has ordered fishermen to stop blocking survey vessels hired by a pulp mill, in a decision that came after protesters chanted their opposition to the firm's plans to pump effluent into the Northumberland Strait.

The temporary injunction, granted by Justice Denise Boudreau in the Nova Scotia Supreme Court, was the latest round in an increasingly tense conflict over a proposal by Northern Pulp to dump over 62 million litres per day of treated waste into the rich fishing grounds.

The company, a subsidiary of Paper Excellence, has said the effluent will meet federal regulations for emissions, but opponents counter there's a lack of firm scientific evidence of how the waste will affect the long-term health of the lucrative lobster and crab fisheries.

Northern Pulp plans to return to court Jan. 29 to seek a long-term injunction.

Allan MacCarthy, one of the fishermen ordered to cease blocking the company's seismic vessel, said outside court that he'll abide by the order. However, he referred to the decision as merely "a skirmish" in his industry's long-term battle with Northern Pulp.

Hours earlier, protesters chanted outside the courthouse: "All I want for Christmas is no pipeline."

Fishermen and members of Pictou Landing First Nation said they'll renew their efforts to stop the pipeline from proceeding.

Warren Francis, a 49-year-old fisherman and member of the Pictou Landing First Nation, said other protests are coming.

"I don't think it will stop us. My First Nation will have to step it up. There's others willing to do the same thing these guys have done," said Francis, referring to the three fishermen appearing in court.

When a small group of pro-pipeline protesters arrived at the scene, police had to intervene as the two sides faced off in a yard in front of the courthouse.

Ben Chisholm, a 65-year-old business agent for the Pipefitters Union, said he came to support the mill's actions because millions of dollars in economic activity could be lost if the mill closed.

"There's more support for keeping the mill open and cleaning it up than there is for closing it," he said in an interview.

In her decision, Boudreau said that while the fishermen have the right to "lawful protest," they don't have the right to prevent the survey vessels from doing their work.

"Lawful protest doesn't include the description of what has been put forward in the evidence," she said during her decision.

She also agreed with the company that the issue is an increasingly urgent matter, as the survey vessels need to do their work before winter ice creates a delay that would last until the spring.

The Nova Scotia government has committed to stopping the flow of effluent to the heavily polluted Boat Harbour lagoon by Jan. 31, 2020. The lagoon is next to Pictou Landing First Nation.

The lagoon has been referred to by a Liberal cabinet minister as one of Canada's worst examples of "environmental racism."

Boudreau cited evidence presented by Northern Pulp's lawyer, Harvey Morrison, of video footage showing blockades of the seismic vessels.

"They have described events as harassment," Boudreau told the court.

"In October and November of 2018, the difficulties were accentuated, the difficulties became more aggressive."

She also noted evidence of threats made both on the water and in social media.

One of the affidavits from Northern Pulp claims the fishermen at one point shouted at the survey vessel that "20 boats were coming to kill," the seismic boat's employees.

The allegations haven't been proven in court.

The judge also said she accepted that stopping the blockade was "urgent," and there was evidence of a serious economic impact if the plant were to eventually close because of the fishermen's actions.

"I accept, at least on an interim basis ... there could be harm here that would be irreparable," she said.

An affidavit submitted by mill manager Bruce Chapman says if the mill closed it would mean the layoff of 277 employee, while 40 nursery and woodlands employees with affiliated companies would lose their jobs.

Chapman said there would be no work for the approximately 600 employees of contractors who harvest wood for the mill.

In addition, the affidavit said the mill supplies about 40 per cent of the logs used by major sawmills in central and eastern Nova Scotia. As well, the mill purchases almost all of the wood chips produced by the major sawmills in the province.

The mill is the Port of Halifax's largest shipper, paying about $78.3 million for wood chips, hogfuel and pulpwood, and provides $44 million to private woodland contractors, according to the company's submission.