Five people were killed and hundreds of houses were burned to the ground during an attack on three Christian villages in Indonesia's Central Sulawesi, residents and the military said.

The villages were in the district of Poso, which has been seen more than two years of sectarian clashes between Muslims and Christians which have left between 500 and 1,000 dead, and tens of thousands homeless.

"Five people were killed in the attack on Silanca, Sepe and Batu Gencu on Monday," said Noldy Tako, of the Christian Crisis Center in the town of Tentena.

He said the three villages were situated some 12 kilometres east of Poso, the main town in Poso district, and that it took place while the heads of the regional police and military commands were both in the town.

He said the villages of Silanca and Sepe were also home to some 1,000 refugees from other areas in Poso. "Two churches were also burned in Silanca while the total number of houses burned in the three villages reaches hundreds," Tako said on Tuesday.

The violence came just a few hours after representatives from both the Christian and Muslim communities met for a second round of peace talks mediated by Indonesian welfare minister Yusuf Kalla in Palu, the capital of Central Sulawesi.

A military spokesman in Poso said the regional military commander was planning to visit the sub-district where the incidents took place. "We are not yet clear what happened in Lage, but some houses sheltering refugees have been reportedly set on fire," said First Sergeant Erwin, declining to give further details. Police in Poso declined to comment.

Following a new upsurge in violence, an army battalion from South Sulawesi and an elite police unit from Jakarta have been dispatched to reinforce security in Poso.