South Sudan President Salva Kiir has sacked two top security ministers, violating the terms of a peace agreement with opposition party leader First Vice President Riek Machar.

Kiir fired the country's defence minister Angelina Teny, who is also Machar's wife, and interior minister Mahmoud Solomon in a presidential order read on state TV late on Friday, Lily Martin Manyiel, the President's spokesperson said on Saturday.

"There is no reason I can give you right now" for their sacking but "it's a normal procedure usually," Manyiel said, adding that no decision had yet been made on their replacements.

Kiir and Machar's forces signed a peace agreement in 2018 that ended five years of civil war that killed 400,000 people and triggered Africa's biggest refugee crisis since the 1994 Rwandan genocide.

Implementation of the deal, known as the Revitalized Peace Agreement for South Sudan, has been slow and the opposing forces have clashed frequently over disagreements about how to share power.

In Friday's decree, Kiir handed the defence ministry to his party, a role which, under the terms of the agreement, is meant to be appointed by Machar's party.

In exchange, the president gave Machar's party the interior ministry.

"The switch... is unilateral and a new cycle of violating the revitalized agreement," said Puok Both Baluang, Machar's spokesperson.

During a visit to South Sudan last month, Pope Francis implored the country's warring leaders to turn their backs on the violence, ethnic hatred and corruption that have stopped the world's youngest country from achieving peace and prosperity.

Edmond Yakani, a leading civil rights activist and signatory of the peace agreement, said in a statement he urged the presidency to explain "why there is an exchange of information that demonstrates the violation of the peace agreement."