PORTLAND – A federal judge ruled Monday that the former owner of the now-defunct HoltraChem Manufacturing Co. plant in Orrington must pay for a study to determine the extent of mercury pollution in the Penobscot River extending all the way to Penobscot Bay.

Depending on what the study finds, the company also may have to fund a plan to clean up the contamination.

In a 30-page ruling, U.S. District Judge Gene Carter ordered Mallinckrodt Inc. to fund the cost of an independent study to determine: the extent of the existing harm to the river and bay south of the plant site; the need for a remediation plan, if any; and the elements of, and schedule for, completion of such a remediation plan.

Previously, Mallinckrodt had announced a plan to clean up six kilometers, or 3.72 miles, of the river near the Orrington plant.

The ruling marked a victory for the Maine People’s Alliance and the Natural Resources Defense Council, which filed the lawsuit two years ago seeking more extensive studies into the degree of mercury contamination of the Penobscot River from Orrington to Stockton Springs and into Penobscot Bay.

“It’s a huge victory under formidable circumstances and odds,” said John Dieffenbacher-Krall, MPA co-executive director, noting that Mallinckrodt was represented by one of the nation’s most powerful law firms. “Finally, there’s going to be action to investigate the true extent of mercury pollution in the Penobscot River from a study to be done that calls for a cleanup that will be executed.”

Mallinckrodt spokeswoman June Fowler said the company is “disappointed with the ruling. Our counsel is reviewing [the order] and we are examining our options.”

The plant, which produced chlorine and other chemicals, had dumped mercury into the river after the plant was opened in the late 1960s. It was closed in September 2000.

Mercury is a heavy metal found to cause extensive negative health effects in people and wildlife. Because Mallinckrodt is the only former owner of the plant still in business, it is being held legally responsible for the pollution.

The judge gave the St. Louis-based pharmaceutical company, working with the groups that filed the lawsuit, until Aug. 30 to flesh out the details of the independent study.

Mallinckrodt, which has not owned the plant for more than 20 years, had argued during the two-week trial in U.S. District Court in Portland in May that contamination of the river had been adequately studied and that the mercury there does not pose a risk to humans or the environment. It called six expert witnesses to testify to that effect. No company officials testified.

But Carter ruled that the evidence presented by an expert witness for the state and national activist groups caused him to conclude that “dangerously high levels of mercury may be present in Penobscot fish and other seafood consumed by the public.”