President Salva Kiir's spokesman told the BBC Mr Machar "has no space here", and should not return to the country before elections in 2018.
Mr Machar, who had become vice president as part of a peace deal, fled the country following heavy fighting in the capital Juba in July.
But on Monday he vowed to return.
Speaking to the BBC from South Africa, Mr Machar said his rebel faction could still negotiate a peace deal with President Kiir.
In July, Mr Machar's bodyguards and President Salva Kiir's presidential guards fought each other, sparking days of violence.
Hundreds of people died and more than 100,000 fled across the border.
The fighting erupted less than a year after a peace deal was signed to form a unity government and end the civil war.
Riek Machar profiled
On Tuesday, President Kiir's spokesman Ateny Wek Ateny told the BBC that Mr Machar "will look for his space as a citizen of South Sudan, but not as a political leader".
Referring to the elections planned for 2018, Mr Wek said: "I don't think that he (Riek Machar) can even think to come (back) before that."
"It is better that Riek Machar stays away from South Sudan political scenes," the spokesman added.
Both President Kiir's and Riek Machar's followers have been accused of perpetrating atrocities during the country's bitter civil conflict.
More than 2.5 million people in South Sudan have been displaced since December 2013.
More on South Sudan's crisis:

Ben Smith, 34, began his charity attempt on 1 September 2015 and ran 284 consecutive marathons in 284 days.
He then developed an umbilical hernia in June which forced him to stop for 10 days to recover before resuming and making up the lost mileage.
Mr Smith, from Bristol, was joined by about 350 people who set off with him at 10:00 BST on his 401st marathon.
The return loop from Millennium Square in Bristol to Portishead is expected to take the runners about seven hours to complete.
Some runners will join the group from Portishead to run the half marathon distance.
Before setting off, he said he was feeling "nervous but excited" and expected the run to be emotional.
"I'm actually aching today, my legs have been alright for the last 101 days and typical, last day, legs ache, back aches, but I've got one day left," he added.
"I'm doing this to raise Â£250,000 for two anti-bullying charities, I was bullied for eight years of my life at school.
"It affected my confidence and self-esteem and that led to me trying to take my own life when I was 18."
2,528,500 calories burned
Â£163,000 raised in sponsorship
10,506 total distance, in miles
9,485 people who've run with Ben along the way
309 locations throughout the UK
101 schools visited
After the run, his team have put together a three-month "cool down" involving a month of back-to-back half marathons, followed by a month of 10km runs and a month of daily 5km runs.
Mr Smith has had to cover an extra 2.5 miles a day to make up for the time lost through injury - missing 10 days of running equates to 262 miles.
After coming out as gay, the runner wanted to raise awareness of the damage caused by bullying and support his chosen charities, Kidscape and Stonewall.
He said: "A key objective of The 401 Challenge has been to involve as many people as possible and create opportunities for children, young people and adults to discuss the difficult topics of bullying and sexuality."
By the time he finishes his last marathon he will have covered 10,506.2 miles.
Mr Smith's challenge took in 309 locations throughout the UK, with the vast majority of his marathons being distance runs organised by local running clubs.
South Sudan's sacked Vice-President Riek Machar no longer has a role to play as a political leader in the country, the presidency says.
[NEXT_CONCEPT]
A runner who battled a back injury is set to complete his challenge of running 401 marathons in 401 days.