Mayor Luigi Brugnaro said he was forced to ask police to block off the famous St Mark’s Square, which was already covered in knee-high water on Friday morning.
Workers in thigh-high boots began removing the platforms used by the public to cross the square without getting wet.
On Thursday, the government also approved 20 million euros in funding to help Venice repair the most urgent damage.
Venice’s mayor said the damage is estimated at hundreds of millions of euros and blamed climate change for the “dramatic situation” in the historic city.
He called for the speedy completion of the city’s long-delayed Moses flood defence project.
Tuesday’s devastating floods have reignited a long debate on Moses, a multibillion-euro flood defence project that has been under construction since 2003.
The project has not yet been activated, after being delayed a number of times due to corruption scandals, cost overruns and environmentalist opposition over its impact on Venice’s lagoon ecosystem.