Businessman Yorgen Fenech was rearrested on Friday after being granted police bail the previous night, Times of Malta understands.
His rearrest took place after he accompanied investigators to a search of his yacht in Portomaso marina in St Julian's.
Police are questioning him in connection with the murder of Daphne Caruana Galizia, who was killed in a car bomb in October 2017.
Prime Minister Joseph Muscat said investigators had chosen to release Mr Fenech on police bail the previous night as they needed more time to question him before pressing charges.
"Once police prosecute someone, they do not have the right to further question him,” Dr Muscat said.
The prominent businessman was first arrested early on Wednesday morning as he attempted to leave the marina on board his yacht, the Gio.
Dr Muscat subsequently confirmed him as a “person of interest” in the murder case.
Police have yet to make any official statement on the arrest or developments this week.
However investigators were seen back at the Gio on Friday morning with Mr Fenech, who wore a black coat and trousers as well as black sunglasses.
Officials from European law enforcement agency Europol were also spotted on board.
Meanwhile the alleged 'middleman' in the murder case, Melvin Theuma, who has been offered a presidential pardon in exchange for information on the murder case, admitted himself to hospital on Friday.