A top army commander in the troubled new nation of South Sudan has been arrested over a string of alleged human rights violations, officials said Tuesday.

General James Otong Riek was a commander in the eastern state of Jonglei, the scene of heavy fighting last month between rival ethnic groups. The army said he had been implicated in "several reports and complaints of killings".

Over 100,000 people were affected during the July fighting, when thousands of gunmen from the Lou Nuer tribe in northern Jonglei marched south towards Pibor, an area of their rivals, the Murle.

Local authorities told the United Nations that over 300 people died in those clashes, although the total killed has not been officially confirmed.

Army spokesman Philip Aguer gave no further details on the exact charges against Riek, but the general was in command during recent rounds of controversial disarmament campaigns criticised by rights groups for widespread abuses.

He said his arrest had been ordered by President Salva Kiir.

Soldiers were reported to have raped, tortured and looted as they confiscated weapons.

South Sudan's rebel-turned-official army has also been fighting in the region to crush a rebellion led by David Yau Yau, who comes from the Murle people, since 2010.

In May, soldiers and other gunmen looted UN and aid agency stores in Pibor, including a key hospital.

Medical aid agency Doctors Without Borders (MSF) said that many of those who fled the fighting in July are "still hiding in fear in the bush" around Pibor.

The onset of heavy rains in the impoverished and remote region is adding to the woes of the tens of thousands displaced by the unrest.

"As the rains intensify and the living conditions become ever more precarious, the situation in Pibor county remains critical," MSF said in a statement.