The petition, organised by an international association calling for greater protection for Venice, has been sent to Matteo Renzi, Italy's Prime Minister, and Dario Franceschini, the Heritage Minister.
"For more than 13 centuries Venice has survived flooding, disease and war," the petition reads. "But now, in a period of peace, the Queen of the Adriatic, listed by Unesco as a World Heritage site, risks being overwhelmed by these enormous cruise ships, which enter the lagoon on a daily basis, indifferent to the dangers that they bring."
The debate over whether to allow the ships to pass through the lagoon on their way to the international passenger terminal at the western end of the island has raged for years.
Last year the Government proposed banning liners of more than 96,000 tonnes but the decree was overturned by a regional tribunal.
The court, in the Veneto region, ruled that alternative routes for the ships to reach the terminal had not been agreed and that the risks posed by the vessels had not been proved.
The decision was a victory for the cruise ship industry. More than 600 cruise ships dock in Venice annually and the industry says they provide much-needed jobs and revenue.