"The President of the Republic is committed to South Sudan which is multi ethnic, multi religious, multi races and will not directly or indirectly engage in ethnic cleansing," presidential press secretary Ateny Wek Ateny told a press briefing.
Machar has reportedly accused the Kiir's government of ethnic cleansing and trying to sabotage peace talks.
Ateny dismissed the accusations as "utterances from a desperate rebel leader."
"Instead, Dr. Riek and his army, which is exclusively one tribe's army, are by no means free from committing genocide against innocent citizens of particular tribe," he said.
The Nuer tribe and Kiir's Dinka tribe represent South Sudan's two largest tribes.
Together, they account for some 80 percent of the fledging country's total population of 11 million.
The country has been shaken by violence since mid-December, when Kiir accused Machar of standing behind a failed coup attempt against his regime.
Following weeks of talks, the warring rivals signed an agreement last week calling for a cessation of hostilities.
The violence has already claimed the lives of more than 10,000 people.
Concluding a three-day visit to the country, Amos Valerie, UN undersecretary-general for humanitarian affairs and emergency relief coordinator, said Wednesday that some 3.7 million people in South Sudan were now severely food insecure, while more than 820,000 had been displaced.
The presidential spokesman also rubbished calls for President Kiir to step down.
"This was none other than Riek's illusive political ploy," he said.
"President Kiir was elected, and only through ballot can he be made to step aside should the people of South Sudan choose another leader in a free and fair election," he asserted.
"Gun threats and lunatic political desperation from a rebel leader, inspired by prophecy of doom, shall not deter President Kiir's resolves to seek second term in office," said Ateny.