Singh said that Indian officials were questioning the 39 North Koreans on board the ship.
The incident comes in the wake of a UN resolution, passed in June, that allows other countries to request boarding and inspection of North Korean ships suspected of transporting illicit cargo, though the vessels are not required to grant the request.
The resolution was passed to punish the North for its recent nuclear and missile tests.
The MV Mu San picked up its cargo at a port in Thailand, and was also thought to have made a stop in Singapore.
"What also made us suspicious was that their passports were not stamped in Singapore and they were not very clear about their destination," Singh said.
North Korean ships have in the past been accused of clandestinely ferrying nuclear materials, missile parts and arms to trouble spots across the world.
The US Navy tracked a North Korean cargo vessel, the Kang Nam 1, in June. The ship, which was believed destined for Myanmar, suddenly turned back on June 28.
North Korea is believed to earn money from selling its missile technology and weapons.