Joya's criticism of the Mujahideen disrupted the meeting
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A female delegate at a constitutional convention in Afghanistan is under United Nations protection after publicly denouncing warlords.
Malalai Joya received threats after accusing mujahideen of dragging the country into war and calling for them to face trial.
Dozens of angry mujahideen delegates demanded her removal from the session.
The United Nations and Amnesty International have condemned the threats against Ms Joya.
Criminals to lead?
Ms Joya said the mujahideen - fighters who fought against the Soviet Union and then among themselves - were responsible for Afghanistan's civil war which only ended when the Taleban seized power in 1996.
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Why have you again selected as committee chairmen those criminals who have brought these disasters for Afghan people?
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Decrying the selection of the fighters as committee chairmen at the council, she said they had made a mess of ruling the country and should not be allowed into leadership positions again.
She asked the delegates: "Why have you again selected as committee chairmen those criminals who have brought these disasters for Afghan people?"
"In my opinion, they should be taken to court."
Some delegates applauded, but others called for her expulsion and made threats to her life.
Reaction criticised
Amnesty said in a statement: "Some present were heard to say that they would kill the woman while others intervened to protect her."
The loya jirga is forging Afghanistan's political future
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"If delegates are threatened or otherwise prevented from expressing their views, this process of building Afghanistan will be severely threatened."
Although Ms Joya attended Thursday's session, she has moved from the compound housing delegates and is staying in a guarded UN facility.
A UN spokesman acknowledged she was under their protection but declined to say where.
The spokesman, Manoel de Almeida e Silva said the UN deplored Wednesday's incident in which Ms Joya was nearly expelled and was discussing the matter with various parties to try to resolve the issue.
The incident threatens to disrupt the work of the council, which is meeting to debate and ratify a new constitution that will set Afghanistan on a road to democratic elections.