Eastern Sicily, eastern Sardinia and southeast Calabria were all under the civil protection department's highest weather alert as violent storms lashed Italy's southern coast.
Storm Harry has brought winds exceeding speeds of 120km/h, coastal storm surges and torrential rainfall.
Three hundred millimetres of rain was expected over the course of 48 hours in some areas, according to Sky Italia – more than the amount typically seen in three months.
Waves measuring over nine metres in height were recorded on the coast of Messina, northeast Sicily.
Local authorities across all three regions have announced closures of schools, universities, parks, sports facilities, public administration offices and cemeteries as a safety precaution.
Ferries connecting Sardinia to the Italian mainland and Corsica and from Sicily's main island to the Aeolian Islands were suspended, along with some rail lines in Calabria.
In Sardinia, several state roads were closed due to flooding. Two people were injured near the Sardinian town of Tortolì on Tuesday morning after a tree collapsed onto their car as they drove along state highway 125.
In Sicily, an elderly man who drove down a road along the Santa Teresa di Riva seafront that had been closed off due to storm damage was injured after his car fell into a sinkhole.
He managed to contact the emergency services for help and was rescued from his vehicle and taken to a hospital in nearby Taormina.
The region's Civil Protection Chief Salvo Cocina criticised the driver for his "reckless" conduct, urging people in the area to exercise the utmost caution and comply with safety ordinances.
Italy's fire and rescue service said its members had carried out 380 rescue operations in Sicily, 170 in Sardinia and 90 in Calabria.
Two shepherds in the Sardinian municipality of Urzulei who had gone missing after a river burst its banks had been found and brought to safety, it said.
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