Former prime minister Datuk Seri Najib Abdul Razak says he has no knowledge on whether the Equanimity super yacht was purchased using funds from 1Malaysia Development Berhad (1MDB).
Najib set up 1MDB when he took power in 2009, but it accumulated billions in debts.
Malaysian Prime Minister Mahathir Mohamad said that Indonesia has handed over a yacht allegedly bought with money stolen from the multibillion-dollar looting of a state investment fund.
Indonesian authorities impounded the boat on a request from the US Department of Justice, which is seeking to seize $1.7 billion of assets allegedly bought with money looted from Malaysian sovereign wealth fund 1MDB.
The announcement came after Najib, who suffered a shock defeat in May elections, was summoned for a new round of questioning by the anti-corruption agency.
Jho Low - full name Low Taek Jho - had no official positions at 1MDB but was said to exert great influence over the fund.
Low, who has so far evaded investigators, issued a statement through his U.S. lawyer on Monday protesting the handover of the yacht as an "illegal act" for ignoring court proceedings in the United States.
Thomas said the Attorney-General's Chambers (AGC) had invoked the Admiralty jurisdiction of the High Court of Malaya in Kuala Lumpur against the superyacht.
Thomas said that as a result of the Mutual Legal Assistance Treaties (MLAs) between Indonesia, the United States and Malaysia, which were activated recently, sensitive and delicate negotiations were conducted at the highest levels of different agencies in the three countries to accomplish the feat.
The Malaysian authorities have revoked his passport and issued an arrest warrant although he has previously denied any wrongdoing.
"The Mahathir regime's illegal act today, ignoring court rulings in legal proceedings in the USA and Indonesia, prove he has no interest in a fair and just process", he said in a statement Monday.
Mahathir said any claimants to the yacht should provide proof that it belonged to them, and where they got the money to pay for it.
The Equanimity's lavish amenities include a helicopter landing pad, plunge pool, gymnasium and a cinema.