Three people have been killed and at least seven are missing after heavy rains struck Chile over the weekend, causing mudslides and water outages.

The rains, which caused rivers to overflow their banks in mountain valleys near Chile's capital, Santiago, have isolated 3,387 people, the Onemi emergency service said late on Sunday.

Emergency officials said waters rushing down from the Andes since Saturday afternoon cut off roads and caused landslides.

READ MORE: Torrential rains leave hundreds stranded in Chile

The supply of drinking water to about 1.5 million households in Santiago has been affected, with the water company Aguas Andinas saying the torrential rains, which came during the country's usually dry summer months, were making repairs difficult.

"We have a complex situation regarding the potable water supply in 33 communities of Santiago which have approximately six million people," said Mariano Fernandez, Chile's interior minister.

Chilean President Michelle Bachelet wrote on Twitter: "Emergency teams are working on the ground to connect with isolated people and re-establish the water supply wherever possible."

In the San Jose de Maipo valley, directly above the city, emergency crews had to clear the roads of debris before residents could evacuate to lower, less mountainous ground.

It was the second major flooding event to hit central Chile in the past year. Last April, heavy rains battered the San Jose de Maipo valley, killing one person and causing major flooding in downtown Santiago after a river breached its banks.