(Adds details, background, U.S. comment on rebels)

By Skye Wheeler

JUBA, Sudan, June 30 (Reuters) - The government of South Sudan ordered Ugandan troops hunting rebels of the Lord's Resistance Army (LRA) to leave its territory on Monday.

South Sudan's Vice-President Riek Machar said the decision was intended to avoid past mistakes, saying soldiers of the Ugandan People's Defence Force (UPDF) abducted and killed a South Sudanese man during anti-LRA operations this month.

"If there are any forces in Sudan that are UPDF, these should move back to Ugandan territory," he told the South Sudanese assembly.

"If the option to fight the LRA is going to be made, (south Sudan) can handle this on its own," Machar added.

Uganda, which has had troops pursuing LRA forces in southern Sudan since 2002, said it would keep its soldiers there to stop the rebels returning to northern Uganda and threatening Ugandan security.

Uganda's military spokesman, Major Paddy Ankunda, said his government had received no formal communication telling its soldiers to leave.

"We have troops in southern Sudan under an arrangement with the government there, because the threat by LRA rebels still exists," he told Reuters.

Uganda's two-decade civil war uprooted 2 million people and destabilised parts of oil-producing south Sudan and mineral-rich eastern Democratic Republic of Congo.

REBELS "RE-ARMING"

At an African Union summit in Egypt on Monday, the top U.S. diplomat for Africa said the LRA's fugitive leader Joseph Kony was re-arming, and said the United Nations should boost its peacekeeping force in Congo to contain or catch him.

Two years of peace talks between Kampala and the LRA broke down in April prompting Uganda, Sudan and Congo to threaten a joint military offensive against the guerrillas, now based mostly in northeastern Congo.

Jendayi Frazer, the U.S. assistant secretary of state for African affairs, said the talks established a mechanism for reconstructing war-torn northern Uganda and had been positive. However, she said LRA violence against Congolese civilians demanded a response.

"We need to pursue other avenues, particularly since we've seen that he has increased his attacks against local villages … forcing into service women, children," Frazer told reporters on the sidelines of the summit in Sharm el-Sheikh.

"He is re-arming himself. He's preparing himself militarily and so we can't just stand by when he is doing that."

Kony and two of his deputies are wanted by the International Criminal Court in The Hague for war crimes including massacres, rapes and the abduction of thousands of children to serve as fighters, porters and sex slaves.

In April, the elusive rebel chief failed to appear on the Congo-Sudan border to sign a final peace deal. (Additional reporting by Frank Nyakairu in Kampala and Daniel Wallis in Sharm el-Sheikh; Writing by Daniel Wallis; Editing by Andrew Dobbie) (For full Reuters Africa coverage and to have your say on the top issues, visit: http://africa.reuters.com/)

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