The owners of the MT Orkim Harmony last had contact with the ship late Thursday, said Noel Choong, head of the IMB's Kuala Lumpur-based Piracy Reporting Centre.
Malaysian media quoted the coast guard as saying the ship was in the South China Sea off Johor state when contact was lost.
Choong said that after the vessel went missing, an alert had been sent out to all ships in the area to guard against attacks.
"We don't know the whereabouts of the ship right now or what happened but it is likely a hijack of the cargo," he said.
Prime Minister Najib Razak posted a message on his Facebook page saying he was "distressed by the news".
"I pray for the safety of the 22-strong crew of which 16 are Malaysians. My thoughts are with their families," he said.
The London-based IMB has warned over the past two years that the waters of Southeast Asia were becoming the world's piracy hotspot amid a rash of attacks on small coastal tankers.
In a quarterly report released in April, it said pirates attacked one such tanker every two weeks in the region's waters in the first quarter of 2015.
Southeast Asia saw 38 pirate attacks during January-March, or 70 percent of the global total of 54, the IMB said in its April report, calling the frequency of regional incidents "an increasing cause for concern."
Piracy in the region had been significantly reduced in the previous decade by stepped-up regional cooperation and maritime patrols, but has re-emerged as a hazard.
Much of the world's trade passes through its shipping lanes such as the Malacca Strait between Malaysia and Indonesia.
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