The Sudan People\'s Liberation Army (SPLA) contends four citizens in the area sheltered the militias in their houses.
Major General Koang Chuol of SPLA Division 4 in Unity State warned that citizens siding with militias would be given the same treatment as the rebels themselves.
Mayom County Commissioner Charles Machieng Kuol confirmed that another attack carried out by the SPLA against militias on 20 May burned nearly 8,000 homes to the ground.
Kuol said he strongly condemned this destructive activity.
\"The SPLA is responsible for protecting civilians, rather than being against them.\"
He appealed to Unity State Governor Taban Deng Gai to do something about \"these barbaric acts\". The governor has reportedly denied any knowledge of the incident.
Kuol urged the state and national parliament to discuss ways to help residents who lost their homes.
General Chuol confirmed SPLA forces started the flames due to \"crossfire\". He denied that it was a deliberate decision, calling it a \"mistake\" during fighting with the rebel militias.
Following recent deadly clashes in the region, the United Nations Mission in Sudan (UNMIS) expressed deep concern over the heavy loss of life in Unity State, which borders northern Sudan.
Fighting that broke out between the SPLA and militias loyal to the South Sudan Liberation Army (SSLA) has since spread to neighbouring Warrap State.
The SSLA is led by Peter Gatdet Yaka, a former SPLA general who defected to form his own army.
Earlier clashes this year have left hundreds of people dead.
The UNMIS strongly condemned the practice of targeting civilians with heavy caliber weapons and land mines, saying such activities are serious violations of basic human rights and international law.
UNMIS urged all parties to find a means to conduct peaceful negotiations and refrain from violence.