Floodwaters have struck the Italian city of Venice, submerging some of its most famous sites, as its flood defences failed to engage and storms continued to lash large parts of the country.

The city was bracing for a high water level of 145 centimetres, Mayor Luigi Brugnaro said on Twitter.

St Mark’s Square was under water already.

He noted that the city’s flood defence system, MOSE, was not operational.

The system only had its first run earlier this year, when it protected the city from flooding in October.

A flooded St. Mark’s Square. Photo: AAP

It was not clear why MOSE wasn’t operating on Tuesday.

The mayor had only just praised it on Sunday for its effectiveness amid the heavy rains.

He also noted that it had held back two tides since Sunday.

The feared high water level for the city meant that Venice was facing an alarm level of red.

Weather forecasts predict water levels could hit 135 centimetres on both Thursday and Friday.

A high water or Acqua alta phenomenon has taken place in the winter in Venice. Photo: AAP

Luca Zaia, the president of the region of Venice, said damages might amount to 500 million euros ($A818 million).

The risk of landslides and avalanches remains high across the country after recent heavy rains and snowfall.

Parts of South Tyrol are at the second-highest level of risk, authorities said on Tuesday.

Northeast Italy and Rome were on the highest warning level, red, according to emergency officials.