Sicily braced for the arrival of a cyclone Thursday, the second this week after a deadly storm hammered the southern Italian island, killing three people. 

The Mediterranean cyclone known as a "medicane" was set to reach Sicily's eastern coast and the tip of mainland Calabria between Thursday evening and Friday morning, Italian public research institute ISPRA said.

The civil protection unit placed eastern Sicily under an orange alert in anticipation of the storm's arrival. 

"Heavy rainfall and strong sea storms are expected on the coast, with waves of significant height over 4.5 metres (15 feet)," ISPRA said. 

On Tuesday, parts of eastern Sicily off the tip of Italy's 'boot' were ravaged by a cyclone, following days of heavy rains that sparked flooding and mudslides, killing three people.

Television images from Tuesday showed flooding in the emergency room of Catania's Garibaldi-Nesima hospital, while rain was seen pouring from the roof inside offices at the city courtroom. 

Thursday's storm was set to hit the same area around Catania, Sicily's second-largest city, even as residents were still mucking out their streets and homes.

Schools were closed in Syracuse and Catania, where the local government ordered public offices and courts closed through Friday.

Antonio Navarra, president of the Euro-Mediterranean Center on Climate Change, told Corriere della Sera newspaper this week that Sicily was at the centre of extreme weather events, including heatwaves and cyclones. 

"We're trying to understand if, with climate change, these phenomena will become even more intense, if they will change their character as their frequency intensifies," he said.  

The Coldiretti agricultural lobby cited extensive damage to Sicilian citrus groves and olive trees, and estimated that the damage to crops and infrastructure caused by extreme weather events had already cost farmers across Italy two billion euros ($2.3 billion) this year.