A large cloud of dust was seen moving towards the hotel about 2.45pm, after which the miniature tornados whipped through the area.
Publican Dave Gillespie said he and wife Dawn were having lunch at the back of the hotel when they heard glass bottles breaking and saw two small tornados approach from the northwest and hit the building.
About a quarter of the hotel's roof was lifted off, and landed on the road and several vehicles parked outside.
The vehicles were scratched and slightly dented.
Some of the iron hit power cables, sparking wires and temporarily cutting off electricity to the hotel and some surrounding properties.
Tables and chairs in the hotel's garden bar were tossed around and some sheets of iron were blown part-way across a gully on to hilly paddocks about 1km away.
Police and firefighters diverted traffic while Delta Central staff attended to power lines.
Mr Gillespie said builders would temporarily secure the roof so water could not get inside and an insurance inspector would assess the damage.
Bannockburn resident Jimmy Stewart, who was at the hotel yesterday when the tornados hit, said a similar incident occurred in the town about four or five years ago.
In that instance, a neighbour's garage roof was ripped off and blown about 80m up the road, into his property.
"It completely blew off and hit our house before going over our roof and landing in our driveway," he said.
