The men were charged with illegal possession of weapons and ammunition and entering India's territorial waters without permission, Singh said.
"The crew and security guards are cooperating with the investigators," she said, adding that information about the case had been shared with representatives from the U.S. Embassy in New Delhi.
The embassy said it had no comment on the matter.
AdvanFort's president, William H. Watson, denied that the ship was navigating in Indian waters.
"The Indian coast guard approached us and asked us to follow them into the port. We would never have entered Indian waters otherwise," Watson said.
He said the company was cooperating with Indian investigators.
The ship had 10 crew members and 25 armed security guards from India, Britain, Estonia and Ukraine. Two of the crew members were not arrested and were allowed to stay on board the ship to carry out maintenance work.
India is very sensitive about the presence of armed security guards on merchant ships after the shooting deaths of two fishermen by armed Italian marines last year. The marines were part of a military security team on a cargo ship when they fired at the fishermen, mistaking them for pirates. The two Italians are facing trial in India for the deaths.