Analysts say the issue threatens a ceasefire signed last week.
Officials announced earlier that seven politicians were being charged over an alleged coup attempt in December.
It was initially a political dispute between President Salva Kiir and his former deputy Mr Machar on 15 December.
Since then, violence has spread into a full-scale conflict, with reports of ethnic killing.
Eleven officials, who are prominent political figures from a faction of the governing SPLM party, were arrested at the time of the alleged coup.Four have been charged with treason and seven have now been released to the authorities in Kenya, where they appeared at a news conference on Wednesday with Kenyan President Uhuru Kenyatta.
On Tuesday evening, South Sudan's justice minister said the treason charges would be brought against four men who were already in custody, plus three men on the run.
"I personally have not planned a coup and my colleagues who are under detention have not planned a coup with me so I see no reason why we would face such charges, Mr Machar said.
The government should differentiate between the alleged coup and the current rebellion.
With peace talks expected to begin in February, Mr Machar said he hoped the regional mediators would live to their commitment and free the four men still in detention.
These comrades are important in the peace process,Mr Machar said.
Mr Machar, who was sacked as Mr Kiir's deputy last July, has been on the run since 15 December and has refused to say where he is hiding.
Before Thursday's ceasefire, he said he had come under attack several times from South Sudanese and Ugandan soldiers, who are fighting alongside government forces.
Both sides say they are committed to the ceasefire, but there is still fighting in some areas, and the United Nations has described the situation as fragile.
More than 646,000 people have been displaced since the fighting began in mid-December
Aid groups say up to 10,000 people have been killed in the conflict.
The UN says more than 646,000 people have been displaced inside South Sudan and more than 123,400 people have fled to neighbouring countries.
The UN's aid chief Valerie Amos has wrapped up a three-day visit to the country with a trip to Malakal, where she said some people were afraid to return home despite the truce and had "completely lost faith'' and wanted to be relocated to other parts of South Sudan, or even out of the country.