A man looks at the debris of a burned Christian church on Wednesday in Aceh Singkil, a day after a man was killed in violent clashes that saw a church burned to the ground by hundreds of armed Muslims. (AFP Photo)

Banda Aceh. Thousands of Christians taking refuge after two attacks by a Muslim mob at separate churches in their hometown of Singkil, Aceh, are set to return home on Friday afternoon with the police and army's assistance.

Nasir Zalba, head of the Union of Nations, Politics and Society Protection, told the Jakarta Globe on Friday that 5,490 Christian refugees from Singkil, who have been staying for three days in neighboring districts Central Tapanuli and Pakpak Bharat, would depart using vehicles provided by the police and Indonesian Army.

"Local authorities and officials have met with the refugees. And even though they said they were still worried, they wanted to go back home," Nasir said .

Aceh Singkil district head Safriadi and Aceh Police chief Ins. Gen. Husen Hamidi will monitor the transfer and beef up security to prevent any disturbances, he added.

On Tuesday an angry mob of some 500 Muslims attacked and set a church in Aceh Singkil on fire for allegedly operating without a permit.

A second incident took place at a church in Dangguran village where one assailant was reportedly shot dead and five others injured.

The police have named 10 people as suspects, but only officially detained three in the premeditated attacks and ensuing deadly clash.

President Joko Widodo has condemned the mob attacks, while Home Affairs Minister Tjahjo Kumolo called for regional officials to maintain religious freedom and tolerance.

Churches in Indonesia have seen forced closures by local officials and attacks by hard-line Muslim groups since the republic transitioned into a democratic era known as reformasi in 1998.

However, the issue seemed to have particularly aggravated in the predominantly Muslim Aceh where the shariah law applies.