Uganda's army, backing its neighbor South Sudan against a four-month-old rebellion, said on Wednesday UN peacekeepers should have done more to stop insurgents slaughtering hundreds of civilians there last week.

Uganda sent troops into South Sudan shortly after fighting broke out between soldiers loyal to President Salva Kiir and his sacked deputy Riek Machar in mid-December.

In the latest major violence in the increasingly ethnic conflict, rebels hunted down men, women and children taking refuge in a mosque, church and hospital in oil town Bentiu where the UN has a base, according to a report from the global body.

"It is disturbing that civilians are being killed in the backyard of a UN mission," Ugandan military spokesman Paddy Ankunda told Reuters.

"There are thousands of UN soldiers in the country and you have hundreds killed under their noses ... The United Nations ought to do more to stop these crimes," he said.

"We cannot allow the killings of civilians. These sort of atrocities demonstrate what would happen if we were not there," Ankunda said.

The UN mission in South Sudan, known as UNMISS, has approximately 8,500 military peacekeepers and police deployed in South Sudan.

File photo: UN troops in Pibor, 6 March 2013 (UNMISS/Martine Perret)