The search at the New Jersey port began after a Coast Guard inspection team heard knocking for about two hours that suggested stowaways might be inside one of the boxes.
The US Department of Homeland Security (DHS) said after a thorough search that no stowaways were found inside the containers.
The search operation began yesterday morning after a Coast Guard team heard sounds consistent with humans coming from a container buried under a stack of others.
The container, according to a manifest, was carrying machine parts to Norfolk, Virginia.
It was loaded aboard The Villa D'Aquarius in India, Coast Guard spokesman Charles Rowe said.
Officials were aboard the Ville D'Aquarius conducting a thorough investigation of the vessel.
The ship is reported to have started its journey on May 30 in the United Arab Emirates. Thereafter, it made one stop in Pakistan, two in India and final one in Egypt on June 15.
The ship docked at the Port Newark yesterday and soon the boarding party heard knocking sounds coming from the container.
According to local 'Star Ledger' in New Jersey, Walter Arsenault, Executive Director of the Waterfront Commission of New York Harbor, said he was told that inspectors focused on the 210 containers on board the ship, where Coast Guard crew members said they believed the noises originated.
During an inspection, the boarding team was conducting a sound check and when they knocked on one container, they heard a knocking back.