Indian authorities have registered a case against all 35 people on board the US ship Seaman Guard Ohio, which was seized by officials at the port of Tuticorin for carrying weapons and ammunition without valid documents.
The Sierra Leone-flagged vessel, operated by the US-based anti-piracy security firm AdvanFort, was earlier detained by officials for sailing in Indian waters without permission.
The 10 crew members and 25 armed security guards on the ship were charged under the Indian Arms Act 1956, which prohibits illegal possession of arms and ammunition. Further movement of the vessel has also been restricted until the ship is cleared for sailing.
The ship is said to have carried sophisticated semi-automatic weapons along with more than 5,700 rounds of ammunition.
"When they enter the exclusive economic zone of a country, they should get proper permission to carry weapons. They didn't have documents of authorisation," said senior official at Coastal Security Group Sylendra Babu, according to the Times of India.
Officials in New Delhi have sought more details from local authorities on the incident, but a probe by the anti-terror National Investigation Agency has been ruled out.
"We have asked for a detailed report. Since it was carrying arms and bought fuel in India illegally, we have asked the agencies for a thorough probe into the matter," said a spokesperson from the ministry of home affairs.
Meanwhile, the US security firm has thanked the Indian authorities for "allowing the vessel... to enter the port both to take on fuel and to escape the effects of Typhoon Phailin".
India's east cost was recently battered by the powerful cyclone.
In a press release sent to IBTimes UK, the president of AdvanFort International, William Watson said: "I want to personally thank the Indian government for offering a safe harbour during this typhoon to the crew of our good vessel OHIO. We look forward to returning this vessel to its duties as quickly as formalities and resupply operations are concluded."
Watson added: "As these men [crew and security guards] routinely provide armed counter-piracy protection, they also had aboard their uniforms, protective equipment, medical kits, rifles and ammunition - all of which is properly registered and licensed to AdvanFort."