The United Nations announced the dismissal of Lt. Gen. Johnson Mogoa Kimani Ondieki, of Kenya, shortly after the report was released Tuesday.
The report assesses the response to an outbreak of clashes in Juba between forces loyal to President Salva Kiir and those loyal to rebel leader Riek Machar.
More than 70 people were killed in three days of fighting, the report said, and 182 buildings in the UN headquarters, which house more than 27,000 displaced people, were struck by bullets, mortars and rocket-propelled grenades.
The report said peacekeepers failed to respond to an attack on civilians at the Terrain compound, a private compound less than a mile from the UN compound. About 70 UN personnel, aid workers and local staff were inside when government soldiers forcibly entered the camp on July 11, the report said. It had been on lockdown for days.
Between 80 and 100 South Sudanese soldiers attacked the compound that housed mostly foreign staff and carried out repeated rapes, mock executions, lootings and killings, according to several reports.
Witnesses told CNN horrific stories
of the attack. They said the UN mission did not respond to repeated requests for help.
"During the attack, civilians were subjected to and witnessed gross human rights violations, including murder, intimidation, sexual violence and acts amounting to torture perpetrated by armed government soldiers," the report said.
In one example, the report said one international female humanitarian worker at the Terrain camp called UN security after most of the others were rescued, but the security officer was dismissive of her appeal for help and did not call her back when her phone credit expired.
Lack of leadership
Ban said he was alarmed by the report, according to a statement issued by his office.
The special investigation team, led by retired Dutch Gen. Patrick Cammaert, identified serious shortcomings at the UN Mission in South Sudan.
- An overall lack of leadership, preparedness and integration among the various components of the mission.
- A culture of reporting and acting in silos inhibited effective action during a period in which swift, joint action was essential.
- Forces did not operate under a unified command, resulting in multiple and sometimes conflicting orders to the four troop contingents from China, Ethiopia, Nepal and India.
- Peacekeepers were risk-averse.
The UN mission in Sudan has come under repeated criticism in the past for failing to protect citizens.
Doctors Without Borders criticized the UN mission in February when peacekeepers did not intervene in fighting at a Protection of Civilians Site in Malakal, South Sudan.
South Sudan, which gained independence from Sudan in 2011, descended into a two-year civil war in 2013 after Kiir, an ethnic Dinka, accused his vice president, Machar, who is an ethnic Nuer, of plotting a coup.
In August 2015, the warring parties negotiated a peace deal to establish a national unity government, but that largely disintegrated in July when fighting resumed between forces loyal to Kiir and those of Machar after their security forces engaged in a firefight at the presidential complex. Around 300 people were killed in those clashes.
Since the July outbreak of violence, around 70,000 South Sudanese people have crossed the border into Uganda as refugees. Since fighting began in December 2013, more than 2 million South Sudanese have fled their homes, according to the United Nations.