The MT Vier Harmoni, carrying 900,000 litres of diesel, is being searched in Batam Island, Indonesia.
Indonesian Navy spokesman, Edi Sucipto told BBC that the confusion was due to an “internal management problem”. Malaysia also said it was an “internal dispute”.
Earlier, reports said that the Malaysian oil tanker carrying 900,000 litres of diesel had been hijacked and taken to Indonesian waters.
The Malaysian Maritime Enforcement Agency (MMEA) said the Vier Harmoni was believed to have been taken in waters off Kuantan port.
The agency’s director tweeted that the ship was believed to be off the Indonesian Island of Batam.
Its cargo is reportedly worth about 1.57m ringgit ($392,795; £300,000).
The head of the Malaysian Maritime Enforcement Agency said the dispute between the operator and the crew had been resolved but he did not outline what had happened to the ship’s oil cargo, or whether it would sail back to Malaysia.
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