According to TV news channels, the vessel has been detained off the Kolkata coast at the Diamond Harbour.
Officials at the Harbour, who detained the ship on intelligence tip-off, have found ship to be loaded with anti-aircraft guns and rocket launchers, besides ammunition and smoke bombs, reported CNN-IBN.
"It's surprising why the Pakistan-bound vessel was passing through Indian waters," West Bengal's Inspector General of Police (Law and Order) S Karpurakayastha is quoted as saying in the report.
Navy, the Coast Guard and the police cordoned off the ship and are searching it while the documents are also undergoing verification and crew members are being interrogated.
The vessel which was on its way to Karachi from Bangladesh has been registered in Liberia.
Authorities, who have not found any terror link to the ship, believe that it was passing through international waters but strayed into Indian waters.