About 50 protesters dressed in wetsuits managed to delay the ships by more than an hour as they bobbed about in the canal, according to the Daily Telegraph.
Protesters claim the ships are threatening Venice's fragile foundations and want the port moved to an island away from the city.
Around 1,000 protesters lined the banks of the canal on the busiest day of the cruise ship calendar, with 12 ships calling in to the city yesterday.
Silvio Testa, a spokesman for the No Grandi Navi (No Big Ships) campaign told La Nuova Venezia newspaper before the demonstration: "We want to say enough to this situation. St Mark's Basin is like a motorway. Soon we'll have to put traffic lights up."
Following the protests he said: "The demonstration was a great success and we now hope the government will take advantage of this momentum and kick the cruise ships out of the Venice lagoon," reported the Daily Telegraph.
Around 40,000 cruise ship passengers arrived in Venice on Saturday and Sunday. Protesters argue that most head straight for the airport, bypassing the town and contributing nothing to the economy. Whereas supporters say the industry is vital to locals' livelihoods, and a huge source of income.
Italian Environment Minister Andrea Orlando is proposing enacting emergency legislation -- drafted after the Costa Concordia accident -- which would ban ships of more than 500 tons coming within two nautical miles of landscapes of natural or cultural importance. Orlando told the newspaper Il Gazzettino he will put the proposals in front of a cross-party parliamentary committee next month (October).
The move is backed by Venice's mayor Giorgio Orsini, who wants to see cruise passengers dock at a nearby town, Porto Marghera.
--by Adam Coulter, U.K. Editor