Reports that Machar - a longtime rival of President Salva Kiir - was arrested on Wednesday prompted international calls for restraint. Neighbouring Kenya sent its former prime minister, Raila Odinga, to defuse tensions.
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Machar's party said this week that his detention had effectively voided a 2018 peace deal that ended a five-year civil war between Kiir's Dinka forces and Nuer fighters loyal to Machar.
Government spokesperson and information minister Michael Makuei said in a statement that "Machar and his anti-peace colleagues of the SPLM/A-IO (Machar's party), who are under arrest will be investigated and brought to book accordingly."
He accused Machar of contacting his supporters and "agitating them to rebel against the Government with the aim of disrupting peace so that elections are not held and South Sudan goes back to war."
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"The Peace Agreement has not collapsed and shall not under any circumstances," Makuei said.
There was no immediate response from Machar or his party to the allegations.
Machar's party has previously denied government accusations that it backs the White Army, an ethnic militia largely comprising Nuer youths, which clashed with the army in the northeastern town of Nasir this month, triggering the latest crisis.
In response to the fighting, Kiir's forces rounded up several of Machar's senior allies, including the petroleum minister and the deputy head of the army.
There have been clashes in recent days between forces loyal to the two men outside Juba and elsewhere.

--Reuters--