Yorgen Fenech was on a yacht intercepted on a northward course away from Malta by the Maltese military early Wednesday and forced back to port.
In remarks to reporters, Prime Minister Joseph Muscat did not directly tie the arrest to the murder of 53-year-old Daphne Caruana Galizia in a powerful car bomb in October 2017.
But he did say that it appeared to result from comments he made a day earlier on the possibility of a pardon for an alleged middleman who had offered to identify the mastermind of the killing.
The slain journalist's three sons were more direct in their comments on Twitter, making a direct link between the arrest and their mother's assassination.
Muscat said he instructed police to be on the lookout for unusual actions by "people of interest" in the long-unsolved murder, after announcing Tuesday that a pardon would be possible for the middleman if information he provided could stand up in court.
"If I had not given these instructions, maybe today we might be speaking of persons of interest who might have escaped,'' Muscat told reporters.
He declined to comment further out of concern that any comments might prejudice a case.
The prime minister said that no politician is tied to Caruana Galizia's murder. However, tweets by Caruana Galizia's sons ties the arrested businessman directly to Muscat's chief of staff and a former energy minister.
No details of charges against Fenech have been revealed, but authorities would have 48 hours to decide on them.
Fenech is a very prominent hotelier and director of the Maltese power company. His name was on leaked documents as a source of income for companies named in the Panama papers.
Caruana Galizia alleged on her blog eight months before her violent death that a company called 17 Black Ltd. was connected to Maltese politicians, but provided no specific evidence.
That reporting was picked up by the Daphne Project after her murder. It reported in April 2018 that Malta's anti-money laundering watchdog had identified Fenech, the chief executive of a Maltese property developer, as the owner of 17 Black.
The Daphne Project followed a paper trail to two Panama companies in the names of two people close to Muscat — his chief of staff and the former energy minister — that stood to receive payments from 17 Black for unspecified services. There is no evidence the payments went ahead.