Singapore's Maritime and Port Authority (MPA) said in a statement that there were "some injuries" among the crew, with four members unaccounted for.
Photographs taken by a coast guard plane showed a thick plume of billowing black smoke and containers that had seemingly been hurled up by a powerful explosion on board.
"Fire incident reported onboard Singapore-flagged container vessel MV Wan Hai 503," India's defence ministry said in a statement, adding that it had diverted a destroyer to aid the stricken ship.
It said the 268-metre (879-foot) vessel caught fire some 78 nautical miles off Beypore port.
Singapore's MPA said that, of the total crew of 22, 18 had been "accounted for and are in the process of being transferred from lifeboats to a passing vessel", adding that "some injuries have been reported among them".
It said four crew members remain unaccounted for.
"The Indian Coast Guard and Indian Navy are rendering assistance to the crew and conducting search and rescue operations for the missing crew," the MPA said.
A Liberian-flagged container ship with hazardous cargo sank off the coast of Kerala in southern India last month. The Indian navy rescued all 24 crew members.
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