South Sudanese forces have arrested a senior military official allied with First Vice President Riek Machar, and deployed troops around Machar's residence, risking a 2018 peace deal that ended a civil war, his spokesperson said.

South Sudan has formally been at peace since the 2018 agreement ended a five-year conflict between Machar and President Salva Kiir that killed hundreds of thousands of people, but violence between rival communities flares up frequently.

On Tuesday, General Paul Nang, the head of South Sudan's defence forces, arrested one of his deputies, Lieutenant General Gabriel Doup Lam, while security forces surrounded Machar's residence, Machar's spokesperson Pal Mai Deng said in a statement late on Tuesday.

"This action violates the Revitalised Agreement on the Resolution of the Conflict in South Sudan and cripples the Joint Defence Board, a vital institution of the Agreement responsible for the command and control of all forces. This act puts the entire agreement at risk," the statement said.

"We are also gravely concerned about the heavy deployment of SSPDF (South Sudan army troops) around the residence of... Machar," he wrote. "These actions erode confidence and trust among the parties."

Deng did not give a reason for Lam's arrest.

Major General Lul Ruai Koang, the South Sudan army spokesperson, said in a statement late on Tuesday he would not comment on the arrest or the troops surrounding Machar's residence.

Information Minister Michael Makuei did not immediately respond to requests for comment.

The civil war that broke out in December 2013 after Kiir sacked Machar killed an estimated 400 000 people, drove more than 2.5-million people from their homes and left almost half the nation of 11-million struggling to find enough food.

Oil production, a vital revenue source for the impoverished nation, also dropped.

In July 2016, forces loyal to Kiir and Machar fought each other for about five days in the capital with anti-aircraft guns, attack helicopters and tanks, with both leaders denying responsibility for starting the violence and calling for calm while it continued.