Flooded Piazza San Marco square during an exceptional "Alta Acqua" high tide water level.

Venice was hit by the highest tide in more than 50 years late Tuesday, with tourists wading through flooded streets to seek shelter as a fierce wind whipped up waves in St. Mark's Square.

The exceptionally intense "acqua alta," or high waters, peaked at 1.87 metres (six feet) as the flood alarm sounded across the Italian city of canals, the tide monitoring centre said.

"We're currently facing an exceptionally high tide. Everyone has been mobilised to cope with the emergency," Venice's mayor Luigi Brugnaro tweeted.

Only once since records began in 1923 has the water crept even higher, reaching 1.94 metres in 1966.

Tables and chairs set out for aperitifs bobbed along alleyways in the dark, as locals and tourists alike waved aloft inside-out umbrellas, the water slopping over the top of even the highest waders and wellies.

Water taxis attempting to drop people off at the glamorous and historic hotels along the Grand Canal discovered the gangways had been washed away, and had to help passengers clamber through windows.

A room in the flooded Gritti Palace during an exceptional "Alta Acqua" high tide water level in Venice. (AFP)

"It will be a long night," Brugnaro tweeted, saying that as the water level began to drop again "the fears of a few hours ago are now being replaced by an assessment of the damage done".

The exceptional flood was "a wound that will leave a permanent mark", he said.

"Swimming"

A couple of French tourists caught out said they had "effectively swum" after some of the wooden platforms placed around the city in areas prone to flooding overturned.

Antique pieces of furniture could be seen submerged in low-lying hotels and homes.

Since 2003, a massive infrastructure project has been underway to protect the city, but it has been plagued by cost overruns, scandals and delays.

The plan calls for the construction of 78 floating gates to protect Venice's lagoon during high tides.

St. Mark's Square is particularly affected by the high tides, as it is located in one of the lowest parts of the city.

The vestibule of the basilica was inundated with water, and authorities planned to watch the building overnight.

Pierpaolo Campostrini, a member of St. Mark's council, said the scale of the flooding on Tuesday had only been seen five times in the long history of the basilica, where construction began in 828 and which was rebuilt after a fire in 1063.

Most worryingly, Campostrini said, three of those five episodes occurred in the last 20 years, most recently in 2018.

Venice was not alone: powerful rainstorms swept through Italy on Tuesday, hitting the south hard as well.

The heavy rainfall closed schools in several southern cities including Taranto, Brindisi, and Matera, as well as the Sicilian cities of Pozzallo and Noto, according to the national weather service.

In Matera, this year's European Capital of Culture, a tornado caused trees and lamp posts to fall, damaging numerous roofs and buildings. No injuries were reported.