The mayor of Venice has blamed climate change for severe flooding in the historic Italian canal city reaching the second-highest levels ever recorded, with financial costs expected to run to hundreds of millions of euros.

Key points: The city's historic St Mark's Basilica sustained serious damage

The city's historic St Mark's Basilica sustained serious damage A man in his 70s died when he was struck by lightning while using an electric water pump

A man in his 70s died when he was struck by lightning while using an electric water pump Venice's Mayor called for a speedy completion of a long-delayed project meant to limit flooding

The high-water mark hit 187cm late Tuesday (local time), meaning more than 85 per cent of the city was flooded.

The highest level ever recorded was 194cm during the infamous flood of 1966.

A man in his 70s died on the barrier island of Pellestrina, when he was struck by lightning while using an electric water pump, the fire brigade said.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 34 seconds 34 s Venice's Mayor has blamed climate change for the floods in the city. (Photo: Reuters/Manuel Silvestri)

Danny Carrella, an official of the island, said the situation there remained dramatic, with a metre of water still present due to broken pumps.

Venice's mayor Luigi Brugnaro said in a tweet the exceptional flood was "a wound that will leave a permanent mark", which he blamed on climate change.

Photos on social media showed a city ferry, taxi boats and gondolas grounded on walkways flanking canals.

At least 60 boats were damaged in the floods, according to civil protection authorities, including some pedestrian ferry boats.

People walk across a provisional footpath in the flooded St Mark's Square in Venice. ( Reuters: Manuel Silvestri )

Floodwaters inundated the famed St Mark's Basilica, raising concerns about damage to the mosaics and other artworks.

The electrical system at La Fenice theatre was deactivated after waters entered the service area, and firefighters brought under control a blaze in the Ca' Pesaro modern art gallery, caused by a short circuit.

'Venice is on its knees'

Officials said a second exceptional high of 160cm was recorded at midmorning Wednesday (local time), but was quickly receding.

"Venice is on its knees," Mayor Luigi Brugnaro said on Twitter.

"St Mark's Basilica has sustained serious damage like the entire city and its islands."

People assess damages in a wing of St Mark's Basilica. ( AFP: Marco Bertorello )

Venice Archbishop Francesco Moraglia said the city's historic St Mark's Basilica risked "irreparable" harm.

"The Basilica is suffering structural damage because the water has risen and so it's causing irreparable damage, especially when it dries out in the lower section of the mosaics and tiling," he said.

The head of the Venice hotel association said the damage was enormous, with many hotels losing electricity and lacking pumps to remove water.

Tourists with ground floor rooms had to be moved to higher floors as the waters rose on Tuesday night (local time), the association director Claudio Scarpa told Italian news organisation ANSA.

A man transports his goods through walking through the floodwaters. ( Reuters: Manuel Silvestri )

Mr Brugnaro blamed climate change for the "dramatic situation" and called for a speedy completion of a long-delayed project to construct offshore barriers.

Called "Moses", the moveable undersea barriers are meant to limit flooding of the city, caused by southerly winds that push the tide into Venice.

But the controversial project is opposed by environmentalists concerned about damaging the delicate lagoon eco-system, and also delayed by cost overruns and corruption scandals. There is no launch date in site.

Luca Zaia, governor of the Veneto region, told SkyTG24 that the barriers were almost complete, but it wasn't clear if they would work against such flooding.

"Despite 5 billion euros under water, St Mark's Square certainly wouldn't be secure," Mr Zaia said, referring to one of Venice's lowest points that floods when there is an inundation of 80cm.

Across the Adriatic Sea, heavy storm and sweeping winds also caused floods in towns in Croatia and Slovenia.

ABC/wires