Thirty-three of the crew were taken into custody, while two were left aboard the ship to carry out maintenance work, The Times of India reported.
The MV Seaman Guard Ohio has been docked in Chidambaranar since Oct. 12 when it illegally entered Indian waters off the Tuticorin coast.
Indian authorities found and confiscated as many as 31 assault rifles and more than 5,000 rounds of ammunition aboard the ship. The ship also illegally purchased 396 gallons of diesel fuel.
A complaint against the ship from the assistant commandant of Indian Coast Guard included several offenses, including violations of the Arms Act, 1959, Essential Commodities Act, 1955, and Motor Spirit and High Speed Diesel, 1990, the Hindustan Times reported.
The ship also had no log of the arms, the complaint said.
Indian Deputy National Security Adviser Nehchal Sandhu said he did not believe that the ship was involved in gunrunning.
AdvanFort, the company that owns the vessel, issued a statement on Monday, thanking the Tamil Nadu police for "allowing our vessel, Seaman Guard Ohio, to enter the port both to take on fuel and to escape the effects of Typhoon Phailin."
"I want to personally thank the Indian government for offering a safe harbor during this typhoon to the crew of our good vessel Ohio, said William H. Watson, president of AdvanFort. "We look forward to returning this vessel to its duties as quickly as formalities and resupply operations are concluded."