The US-based rights group Human Rights Watch (HRW) accused the South Sudans People's Liberation Army (SPLA) of deliberately attacking civilian areas, burning and looting homes, and arbitrarily detaining and summarily executing people.
South Sudan has rejected the report in which the organisation highlighted the militarys numerous extrajudicial executions, enforced disappearances, rapes and other grave abuses during its recent counter-insurgency campaign in western Equatoria state.
HRW recorded at least 11 cases of enforced disappearances and extrajudicial executions by government forces between November 2015 and February 2016, in and around Yambio.
The abuses appear to be widespread and systematic attacks on civilians suspected of having links to rebel militias known as Arrow Boys. The violence has taken on an ethnic dimension, with largely Dinka government soldiers targeting non-Dinka locals, the report noted.
The organisation urged the UN Security Council to impose a comprehensive arms embargo on all forces in South Sudan in order to curtail abuses against civilians.
The groups Africa director, Daniel Bekele, said an arms embargo and effective war crimes court are crucial to stamp out abuses and send a message that crimes will not go unpunished.
South Sudans Information Minister Michael Makuei Lueth dismissed the report, describing it as propaganda to derail peace efforts in the country.
The government is stabilising the areas through fighting the so-called insurgencies; these groups claim to be allied with SPLM-IO led by the first vice president designate Dr. Riek Machar, but they have failed to abide by the 2015 August peace deal, and the national army has a mandate to protect the lives and property against any disturbances, Lueth said.
The government has mechanisms in place to hold unruly soldiers responsible, he said. "As I am talking to you now, we have some SPLA soldiers who have been dismissed" because of abuses they committed in one way or another, he added.
South Sudan Army spokesman Col. Marko Mayol said the SPLAs mandate is to protect civilians, not rape or kill them.
There might be some few undisciplined soldiers that misbehave with the community but then the SPLA don't compromise on indiscipline," Mayol said.
Last month, a United Nations report said South Sudans main warring faction were killing, abducting, displacing civilians and destroying property despite a peace deal they both signed to end over two years of violence.
A peace deal signed in August 2015 between President Salva Kiir and rebel leader Riek Machar is stalling amid a dispute over Kiirs reorganisation of the oil-producing country into 28 states.
More than 10,000 people have been killed and over two million displaced after a political dispute within South Sudans ruling party, SPLM, sparked off a civil war in 2013.
According to HRW, fighting between government armed forces, the SPLA, and local armed groups, known as Arrow Boys began in May 2015, and has since spread across Western Equatoria.
Both the South Sudanese government and its armed opposition faction have made commitments to support justice for crimes against civilians since the conflict began in December 2013, but there have never been any domestic investigations into alleged abuses, despite several calls for a probe.