Earlier reports suggested vessel had been taken by pirates.
A Malaysian oil tanker has not been hijacked as earlier reported, but taken to Indonesia by its own crew, officials in both countries say.
The MT Vier Harmoni, carrying 900,000 litres of diesel, is being searched in Batam Island, Indonesia.
Indonesian Navy spokesman Edi Sucipto said the confusion was due to an “internal management problem”. Malaysia also said it was an “internal dispute”.
The tanker was reported missing off Kunatan port, Malaysia, on Monday.
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.