South Sudan leader fires 5 ministers close to opposition
Under a peace agreement signed in August 2015, Kiir headed the government while Machar was given the position of first vice president.
Thirty ministerial posts were distributed between their two parties and others.
But a presidential decree issued on Tuesday showed that cabinet posts including the interior and petroleum portfolios in the oil-rich state had been filled with allies of the new vice president, Taban Deng Gai.
Deng, who leads a faction of Machar's SPLM/A (IO) party, was named vice president by Kiir after being fired as a minister by his own party leader.
Among those removed were water resources minister Mabior Garang, the son of the figurehead of South Sudan's independence movement, and the minister for higher education, Peter Adwok, an influential ex-rebel.
Their sacking strains the delicate balance of ethnicities in the government, analysts said.
Garang is an opposition figure but a Dinka like the president, while Adwok is a Shilluk, a group which has now lost an important voice in government.
Kiir did, however, retain powerful rebel figure Alfred Lado Gore in his government, moving him from the interior ministry to housing.
Machar ally Gore hails from the Equatoria region, where the capital, Juba, is located and which is seen as a hotbed for opposition recruitment.
The move also comes just days after Lam Akol, a minister representing another opposition grouping, resigned with the intention of organising the government's opponents into a more consolidated force, he said, while declaring the peace deal dead.
South Sudan's political tensions date back to December 2013, just over two years after the state achieved independence from Sudan.
Kiir accused Machar of planning a coup, setting off a cycle of retaliatory killings that degenerated into a ruinous civil war.
The two agreed a peace deal and power-sharing arrangement in August 2015, but problems have lurked beneath the surface.
Renewed fighting in July led the UN Security Council to consider a visit this month to Sudan and South Sudan to push for a return to peace efforts. Machar has not returned to Juba since the clashes.