Fans looked on from a bridge near Castel Sant'Angelo as the star sped under them to film the third installment in the action-adventure series, which is a remake of a popular 1960s TV show.
The boats that usually ship locals and tourists along the river, as well as all other traffic, were barred from the historic waterway for the day, said Battelli di Roma, a company running ferries on the Tiber.
Several scenes in the movie are set in Rome, Italian news reports said. After filming a motorboat chase on the Tiber, shooting will move near St. Peter's Square and in the area around the Trevi Fountain, La Repubblica daily said.
Before stepping into the speedboat, Cruise kissed and embraced actress Katie Holmes (search) on the riverside set. The two became engaged last month after Cruise proposed at the Eiffel Tower in Paris.
"Mission: Impossible 3" is directed by J.J. Abrams (search), one of the creators of ABC's "Lost" and "Alias," and is produced by Cruise and his partner, Paula Wagner.
The movie will feature Cruise and co-stars Ving Rhames, Jonathan Rhys Meyers, Michelle Monaghan and Philip Seymour Hoffman. It is set for release on May 5, 2006.
The first "Mission: Impossible" movie came out in 1996 and was directed by Brian De Palma. John Woo directed "Mission: Impossible 2," released in 2000.