ANCHORAGE — A petroleum company under investigation for leaks in two underwater pipelines in Alaska’s Cook Inlet confirmed Friday it has an issue with a third.

Hilcorp Alaska LLC shut down a natural gas pipeline last weekend when volumes of natural gas moved from a production platform did not match what was received by a processing facility on shore.

Hilcorp shut down the line after “a discrepancy in the metering,” said spokeswoman Lori Nelson in a prepared statement. Flights over the line did not detect gas bubbling, but as a precaution, Hilcorp emptied the line, Nelson said.

“The line now contains filtered seawater,” she said.

Cook Inlet stretches 180 miles (290 kilometers) from the Gulf of Alaska to Anchorage and is home to an endangered population of beluga whales. The inlet provides habitat for humpback whales, the western population of Steller sea lions, northern sea otters and important salmon populations.

Hilcorp began a comprehensive look at all of its Cook Inlet pipelines after the discovery of a natural gas leak Feb. 7 off the east side of the inlet, Nelson said. Hundreds of thousands of cubic feet of processed gas continue to spew from an underwater pipeline that supplies four production platforms. Hilcorp says the gas leak will be repaired after floating ice no longer poses a threat to divers who would perform repairs.

The company also is investigating an oil spill April 1. Workers on the Anna Platform “felt an impact” and spotted an oil sheen and gas bubbling near one of the platform’s legs.

Hilcorp Alaska shut down production on the platform. Based on the size of sheens, Hilcorp estimates less than three gallons of oil spilled.

The source was announced as an 8-inch (20-centimeter) pipeline that runs between the Anna Platform and another platform.

Nelson, however, said Friday that Hilcorp believes the pipeline did not leak the oil. “Hilcorp’s in-line inspection of the line in June of 2016 as well as recent onsite visual inspections showed the line to be in good working condition,” she said.

The low volume of oil is another indication it did not come from the pipeline. Hilcorp does not have an alternative theory for the source.

“It’s under investigation,” Nelson said.

The U.S. Pipeline and Hazardous Materials Safety Administration on Thursday issued a corrections order for the oil pipeline and said it cannot be reactivated without authorization from the agency.

The agency called for a pressure test, visual examination and a restart plan. The agency strongly urged, but it did not require, that Hilcorp develop a safety management system for its pipeline infrastructure in Cook Inlet within a year.

Environmental groups said the incidents show Hilcorp does not have good control over its pipeline system. A “metering discrepancy” is a euphemism for a probable leak, said Lois Epstein, Arctic program director for The Wilderness Society.

“And why are we hearing about this problem from Hilcorp today when they started addressing the discrepancy on Saturday?” she said by email. “Are there other Cook Inlet problems they haven’t told the public about?”

The Center for Biological Diversity on Thursday formally petitioned federal and state regulators to inspect all offshore pipelines in Cook Inlet for corrosion and other damage.