"The preliminary assessment is the vessel was not hijacked but was taken by the crew back to Batam," the Indonesian navy said in a statement in reference to the island near Singapore.
The navy said the captain had contacted its agent twice to say the vessel was returning to Batam because of an internal management problem within the company.
The incident is "linked closely to internal problems between the (Indonesian) owner, the (Malaysian)charterer and the (Indonesian) crew," said Mohamad Taha Ibrahim of the Malaysian Maritime Enforcement Agency.
"Initial investigations on the MT Vier Harmoni revealed that the ship was hijacked due to internal problems," Ahmad Puzi Kahar, Malaysian Maritime Enforcement Agency chief, said in a tweet.
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He did not elaborate, but the phrase "internal problems" has been used in the past to refer to involvement by a ship's crew.
Puzi added that the ship was transporting diesel worth about 1.57 million ringgit (USD 392,000).
A scourge for centuries, piracy in Southeast Asian had been significantly reduced over the past decade thanks to stepped-up regional cooperation and maritime patrols.
In June 2015, pirates commandeered a Malaysian-flagged tanker in the South China Sea for a week before escaping from the vessel in a lifeboat.
But the London-based International Maritime Bureau reported last month that improved security at designated anchorages in Indonesia led to a decline in low-level theft targeting ships in its waters.
According to the IMB, in the first six months of 2016 the number of incidents dropped to 24, compared with 54 during the same time in 2015.