Junainah, a disaster official in Riau Islands province, said the number of fatalities may rise and that communications in the area had been severed, Reuters reported.
"The weather is changing. The wind is still blowing hard. The tidal waves are high," said Junainah, who goes by one name.
The agency said survivors were being evacuated from the Searasan region, while a search and rescue team had been dispatched to the area.
In photos shared by the agency, roofs and trees were seen strewn on the mud-filled ground in heavy rain.
The affected area was on a remote island that was a five-hour boat ride from the capital of Natuna, Indonesia's search and rescue agency said.