"The leadership has decided that for the purpose of promoting dialogue, reconciliation, harmony among the South Sudanese people... I should use my powers to stay the proceedings," Justice Minister Paulion Wanawilla told reporters.
"To stay the proceedings legally means that we have to write to the court to not continue against most of the accused," the minister said, adding that charges against former vice president Riek Machar, who fled the capital and is leading the rebellion, still stood.
President Kiir accused Machar and his allies of attempting a coup, and initially 11 of his loyalists were put on trial. Machar denied the allegation, and in turn has branded Kiir a "genocidal leader" who started the war by carrying out a purge.
Seven of the original 11 detainees were freed in January as part of a regional peace effort, but the release of the remaining four has been a standing rebel demand and their trial has been seen as a barrier to progress in peace talks that have been held in Ethiopia.
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Both sides have been implicated in atrocities and war crimes. Last week the rebels were accused of murdering hundreds of civilians after capturing the oil hub of Bentiu, and a pro-government mob killed dozens of civilians in an attack on a United Nations (UN) base in Bor where they were sheltering.