A fuel tanker that disappeared from a Malaysian port was likely taken by its own crew in a dispute with their employer, Indonesian authorities have said.

The Vier Harmoni, which is carrying 900,000 litres of diesel, sailed into Indonesian waters on Wednesday after it dropped out of contact on Tuesday evening.

Malaysian and Indonesian maritime authorities are still searching for the vessel but ruled out a hijacking, which was earlier reported by several news agencies.

The captain of the vessel twice informed his employer that he was taking the ship back to the Indonesian island of Batam because of an "internal management problem", the AFP news agency reported later on Wednesday.

Al Jazeera's Step Vaessen, reporting from the Indonesian capital Jakarta, said the tanker was near Batam and the crew were believed to have "no intention of selling the oil".

"Malaysian and Indonesian authorities are not calling this a hijacking, or an act of piracy; they're calling this an internal dispute," she said.

For years, gangs of armed thieves have targeted small tankers operating off Southeast Asian coasts, looking for marine diesel and oil to steal and then sell.

"The Indonesian crew on the Indonesian boat took the tanker - full of oil - back to Indonesia after not being paid for well over a month. It was a Malaysian company that chartered the boat but it's a dispute between the Indonesian owner and the Indonesian crew," our correspondent said.

The ship had sailed from the Tanjung Pelepas port, in Malaysia, on Monday.

In June last year, pirates hijacked the Orkim Victory, a Malaysian tanker, and pumped the oil from it into another tanker before releasing it.