The MSC Divina (Divine), which the actress christened last month in France, is a 139,500-tonne ship that can carry 3,500 passengers and nearly 1,000 crew.
"We can't believe that you want your name, which is a legend in Italy and the world, to be associated with a ship that contributes to the destruction of Venice, part of humanity's heritage," said an open letter from the group, called the No Big Ships Venice Committee.
"We are asking you to give up your role as godmother of the ship. Venice and the world would see that as a divine gesture. Venice belongs to the world. Help us save it," the group said in the letter to the Italian screen legend.
A handful of protesters held up a banner that read "No Big Ships" as the Divina passed by St Mark's Square on Saturday.
The letter to Loren said the big ships pollute the air and their vibrations and the lapping waves caused by the wakes of their passage hurt the foundations of historic palaces and churches.
"Venice and its lagoon are both world heritage sites and risk an environmental disaster every day because of the passage of these monsters of the sea," the letter said.
Italia Nostra (Our Italy), the country's leading conservation group has also long been opposing the entry of large cruise ships into the lagoon.
The Divina has a first-class suite named after Loren which is decorated with large pictures of the Oscar-winning actress at various stages of her film career.