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In all four people have died in flooding that forced part of the country's main north-south highway to close and has damaged many homes and shops as well as thousands of acres of farmland.
Tuscany was particularly badly affected, with 800 people evacuated from their homes in the village of Albinia, thousands left without electricity and several towns isolated by swamped roads. The main A-1 highway was closed in parts of the region.
Floods in the Tuscan district of Massa Carrara had caused 10 million euros of damage, according to Italian agricultural group Coldiretti, to farms, crops and olive groves.
The Tiber river burst its banks north of the capital of Rome as heavy rain moved south, flooding factories and homes near the ancient town of Orte.
"Even if you listen to the oldest inhabitants this has never happened before," said Orte resident Luca Seccese. "It has completely destroyed us."
The centre of Rome was kept safe by high embankment walls and because there had been no heavy rain there for two days.
Water levels were receding in Venice, the lagoon city and UNESCO World Heritage Site that at the weekend saw its sixth-highest water levels since records began in 1872.
St Mark's Square, one of the lowest lying areas of the city, where some tourists were able to swim in high water on Sunday, was returning to normal, a city official said.