Minister of Social Affairs Bachtiar Chamsyah confirmed Megawati's planned visit, saying she would meet briefly with victims of the violence.
"The President will take a look at houses (of the victims), which have already been rebuilt in Poso," Antara quoted Bachtiar as saying after meeting the President at the State Palace in Jakarta.
Bachtiar said the government had rebuilt 10,000 of around 15,000 houses destroyed in the fighting between Muslims and Christians since 2000.
Each family affected by the violence would also get Rp8.75 million in compensation from the government, he added.
Burhanuddin Maragau, spokesman for the Poso administration, said Megawati would also present humanitarian assistance to 1,000 victims of the violence during the HKSN celebration.
Megawati's planned visit to Poso comes more than one year after the warring factions signed a truce on December 19, 2001, in the hill resort of Malino, South Sulawesi.
Though the agreement has significantly reduced the levels of violence that has claimed about 2000 lives and forced thousands of others to flee, sporadic violence still erupts.