While Bendigo escaped most of the more severe weather, areas south of the city were affected. 

More than 17,000 households across the state were affected by blackouts. Powercor customers in Taradale, Faraday, Castlemaine, Guildford and Elphinstone remain without power this morning. 

There were also reports of an electrical storm. 

Bureau of Meteorology forecaster Peter Blake said Bendigo recorded its strongest wind gust of 68km/h about 8.30pm. He said weather reports for areas south of Bendigo were scarce. 

An Eaglehawk man was taken to hospital after two large trees fell on his vehicle at Guildford. 

Castlemaine's Sergeant Mark Herman said the 39-year-old man was travelling on the Midland Highway when the incident happened just before 8pm. 

He said SES units were able to free the man and he was taken to the Royal Melbourne Hospital with non-life threatening injuries. 

Kyneton Sergeant Nicky Goodison said police were called to about five reports of trees down last night.

She said motorists should remain vigil this morning, with SES crews working to clear debris. 

"Motorists should drive carefully and drive to the conditions of the road," Sergeant Goodison said.