More bloodshed is feared in the central district of Poso where at least seven people have been killed in the last week, and hundreds of homes destroyed.
Christian groups in Poso have accused Muslim paramilitaries of the Laskar Jihad organisation of recently entering the area and stirring up violence.
Top security minister Susilo Bambang Yudhoyono said two national police and two military battalions would be deployed in Poso, where troops are already patrolling towns and villages.
He planned to visit the troubled region on Tuesday and report back to President Megawati Sukarnoputri.
"The government has decided to conduct
a security operation ... and search for illegal arms and the
organisation which should not be in Poso," he said.
It was an apparent reference to Laskar Jihad which has been fighting Christians in the Moluccas islands near Sulawesi since last year.
The Indonesian Government's National Human Rights Commission says it expected further bloodshed.
"The situation is critical," said a spokesman, Asmara Nababan. "We are afraid that there is going to be a lot of violence."
Villagers flee
The mainly Christian town of Tentena was surrounded by Muslim fighters who were threatening to attack it, he said.
He said three human rights investigators had been sent to the province to see why the police and military "seemed unable to stop the conflict".
Last year around 200 people were killed in a series of clashes between the Christian and Muslim communities.
In the latest violence, a church official said the Muslim groups had burnt down six Christian villages and forced about 13,000 people to flee. This could not be independently confirmed.
The Reverend Erna Makarensi said she had helped evacuate people from the villages last Thursday.
"There were no security personnel in the area on the day of the attack and the evacuation was fully assisted by the churches," she said.