The police operation is part of an investigation into three people and 10 companies, and apart from the yacht, police seized real estate, luxury cars and company shares.
The Italian Financial Police, who announced the seizure on Monday, did not name the businessman.
According to Reuters, however, a confiscation order from a court in Rome named him as Salvatore Squillante.
Reuters cites a court document, which says Squillante served a community service sentence for filing fraudulent bankruptcy in 1993 and made deals that imply he may be linked to a Rome-based organized crime network.
The yacht, named Black Flame, was originally presented to Mussolini by a friend in the 1930s. It was deliberately sunk in 1943 after the collapse of the Fascist regime so it would not fall into German hands. It was later recovered and restored, and after a series of ownership and name changes, bought by the businessman through one of the companies subject to seizure.
The Financial Police say several other properties seized were rented to a company owned by a main suspect in one of Italy's biggest organized crime trials to date, the "Mafia Capitale", in which prosecutors accused Rome officials, politicians and businessmen of colluding with mobsters to rig public tenders for an array of services.
Police identified the person who rented the property only as "SB", identified by Reuters as Salvatore Buzzi – a convicted murderer who is one of the main Mafia Capitale suspects.
