An unknown number of people died and dozens were injured after a tornado razed houses to the ground in the Czech Republic's southeast on Thursday, rescuers said.

"Unfortunately we can confirm there have been victims, but I can't tell you the exact number," local emergency services spokeswoman Hedvika Kropackova told AFP.

She said the death toll would be in the "single digits" rather than in the dozens, but added that any estimates were premature as people were still trapped under debris.

"The first estimates of the injured mentioned 100-150 people, but as things stand we now expect dozens," Kropackova added.

However, the hospital in the city of Hodonin on the Czech-Slovak border said it had treated up to 200 injured people.

Interior Minister Jan Hamacek tweeted that "all available rescue units are in action or moving to the Hodonin region, where several municipalities have been hit by a tornado."

Austrian and Slovak rescuers were helping out and the Czech army was deployed.

The tornado and hail the size of tennis balls struck several towns and villages including Hodonin, where in addition to causing injuries the extreme weather destroyed a retirement home and the local zoo.

The tornado also caused extensive power outages and traffic disruptions, with fallen power lines closing a major motorway connecting Prague with the Slovak capital Bratislava.

Video footage from the region on social networks showed destroyed buildings and cars, shorn tree stumps and several fires with thick black smoke.

"It's living hell," regional governor Jan Grolich said after visiting the region.

The Czech news agency CTK quoted the mayor of Hrusky as saying that half of his village had been razed to the ground.

The storms passing over the Czech Republic forced Prime Minister Andrej Babis to remain in Brussels following an EU summit as a landing in Prague would have been too dangerous.

In neighbouring Poland, a twister struck the southern Malopolska province on Thursday, damaging roofs and injuring one person according to local media.