PORTLAND, Maine — A federal court has ordered that the Nova Star ferry — which operated between Portland and Yarmouth, Nova Scotia for the past two years — be seized for not paying nearly $200,000 to a harbor pilot company.

The warrant for the seizure of the Nova Star was ordered Friday by Magistrate Judge John Rich III. He also ordered that after the federal marshals seize the ferry that it be put in the custody of National Maritime Services which is a global company that holds seized vessels.

A complaint in federal court had been filed the same day by Portland Pilots Inc., a Portland-based company.

Portland Pilots claims in its complaint that it has provided the Nova Star with piloting services in and out of Portland Harbor for the past two years. From Aug. 17 through Oct. 23 of this year, the Portland Pilots escorted the Nova Star in and out of the harbor 61 times at $3,198 for each service. The ferry was piloted by the company from the Ocean Gateway terminal to off Portland Head Lighthouse.

The amount owed by Nova Star totals $196,000, according to the complaint.

The complaint states that the ferry was still docked in Portland Harbor but that it was expected to leave in the next few days and that is why the request for its seizure was made.

A spokesman for the company, Dennis Bailey of Savvy Inc., issued a statement on behalf of Nova Star on Saturday.

“The company will be settling all of its outstanding obligations, as it always has, in the next few weeks,” he said.

The ship, built in 2014, is 483 feet long and can carry 1,215 passengers, according to Nova Star Cruises website.

On Thursday, the province of Nova Scotia announced it would end its relationship with the Maine-based Nova Star Cruises after two seasons, choosing to negotiate for the 2016 season with Bay Ferries Ltd., which had operated the high-speed Cat ferry between the two ports as well as Bar Harbor from 2006 through 2009.

Mark Amundsen, the chief executive officer of Nova Star Cruises, issued a prepared statement Thursday that the company was disappointed by the Canadian province’s decision.

“We would like to thank the people of Nova Scotia for their support over the past two years, and we will work with the province of Nova Scotia toward a smooth transition to the 2016 operating season,” Amundsen said.

The announcement came a week after Nova Star Cruises received its final subsidy disbursement for the 2015 season, bringing the total it received in subsidies for the two seasons to $31.5 million ($41.5 million Canadian).

The luxury ferry service had missed passenger total goals for both seasons, with fewer than 60,000 passengers after setting a goal of 100,000 in its first season and a goal of 80,000 passengers in its second season.

During the service’s second season, Canadian passenger totals declined sharply as the country’s economy dipped into recession and its currency fell to a recent low, with the Canadian dollar worth about 75 U.S. cents.