Malaysian authorities are seeking to arrest Low Taek Jho, the financier who allegedly bought the Equanimity, a 91 meter (300-foot) yacht registered in the Cayman Islands.
They are linked to SRC International, an energy company that was originally a subsidiary of 1MDB, it said.
Malaysian anti-graft agents questioned embattled former premier Najib Razak on Tuesday ahead of his pre-trial hearing in court in connection with the multi-billion-dollar scandal at state fund 1Malaysia Development Berhad (1MDB).
"The Court issued a Warrant of Arrest against it", he said in a statement yesterday.
Jho Low's yacht, the Equanimity has pulled into Indonesia's Batam Island, where it will await a transfer of hands from Indonesian to Malaysian authorities.
In February US and Indonesian authorities moved to seize the yacht as part of an investigation by the US Department of Justice (DOJ).
The US$250-million (RM1.02 billion) yacht docked at the Boustead Cruise Centre Terminal here at 12.40pm, under heavy escort by marine police.
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The former prime minister turned up at the Malaysian Anti-Corruption Commission Academy in a four-car motorcade at about 5pm on Tuesday, where he was said to have received three notices on the new charges against him. He and the fund have denied any wrongdoing.
The U.S. Justice Department, one of several foreign agencies investigating money stolen and laundered from the 1MDB fund, had listed the yacht among assets it could seize and sell to recover stolen funds.
The charges are related to the transfer of 42 million ringgit ($10.3 million) into his bank accounts from SRC International, a former unit of the 1MDB fund that US investigators say was looted of billions by Najib's associates.
The yacht is among assets that included real estate, jewellery and a Picasso painting that the DOJ says were bought with funds stolen from 1MDB.
It is not yet known what the Malaysian government will do with the yacht, but Finance Minister Lim Guan Eng told reporters on Monday that the public should have a chance to view it before it is put on auction.
A total of $4.5 billion was allegedly misappropriated by top-level 1MDB officials and their associates, according to civil lawsuits filed by the USA justice department.