The 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.
A Coast Guard team boarded the 850-foot-long vessel outside New York Harbor early Wednesday as the ship prepared to dock at Port Newark. They heard sounds consistent with people coming from the container, Rowe said. The boarding party followed protocol and didn't open the container at sea in order to control the situation, Rowe said.
Once the ship was docked, authorities began unloading containers to get to the one that the Coast Guard suspected might have people inside.
The Department of Homeland Security said in a statement Wednesday that officials are conducting a "thorough investigation of the vessel."
Drew Barry, of the Sandy Hook Pilots Association, said he boarded the vessel at 5 a.m., about 20 miles offshore.
Barry, who left the ship at around 9 a.m., said he thought it would take several hours, if not much of the day, to get to the part of the ship, below the hatch cover, where officials heard banging noises.
"There are at least 30 to 40 containers on top of the hatch cover, and I don't know how many more below it," Barry said. "If there are people down there, with no food and water for days, they're probably pretty desperate by now."
Customs and Border Protection agents planned to open the container once it was unloaded.
The ship began its voyage May 30 in the United Arab Emirates, then made one stop in Pakistan and two stops in India. Its last port before Newark was in Egypt on June 15.