A cargo ship from Pakistan — suspected of carrying stowaways — pulled into Port Newark this morning and was greeted by teams of emergency responders, officials said.

US Customs agents and Coast Guard personnel took charge of the scene after Port Authority police swarmed the port at Berth 57 to meet the ship at 8:45 a.m., a PA source said.

The suspect container, which a manifest said was carrying machine parts to Norfolk, Va., was loaded aboard the Ville D’Aquarius in India, Coast Guard spokesman Charles Rowe said.

By 12:30 p.m., authorities using X-Ray equipment, had searched 130 containers and found nothing.

More than a dozen ambulances which had rushed to the scene, have left.

“Nothing is panning out here,” a law enforcement source said.

A PA source said separately: “Found nothing. They are going to continue with cautionary expanded inspections and X-Rays.”

The vessel was stopped at 3 a.m. at a standard checkpoint for incoming ships, the Ambrose Anchorage below the Verrazano Bridge in New York Harbor, Rowe said.

That’s when a crewmember heard knocking coming from inside one of the containers, triggering the alert.

“The boarding team went aboard for a routine inspection. They heard sounds that were consistent with people being inside a container,” Rowe said.

Teams from three separate agencies — US Customs and Border Protection, Port Authority police and the Coast Guard — had initially planned to inspect all 2,039 containers on board, law enforcement sources said.

The ship, which was flying a Cyprus flag, began its voyage May 30 in the United Arab Emirates before making stops in Pakistan, 21 days ago, and then two stops in India, law enforcement sources said.

Its last port before Newark was in Egypt on June 15.

“US Department of Homeland Security law enforcement officers and agents are currently investigating allegations of stowaways on a container ship that arrived in Newark, NJ, this morning,” said Customs and Border Protection spokesman Anthony Bucci.

“Officials are currently aboard the Ville D’Aquarius and are conducting a thorough investigation of the vessel.”

Additional reporting by Bob Fredericks, Lorena Mongelli, Chuck Bennett and David K. Li