South Sudan troops have arrested the deputy head of the armed forces and surrounded the home of Vice-President Riek Machar, threatening the country's fragile peace agreement, Machar's spokesperson said late Tuesday.

General Gabriel Duop Lam, a close ally of Machar, was arrested on Tuesday following days of clashes in the Upper Nile state in the east of the country.

The South Sudan People's Defence Forces (SSPDF), the regular army allied to President Salva Kiir, has accused Duop Lam and his troops of working with rebels in that region, who are predominantly from the same ethnic Nuer community.

Machar's spokesperson Pal Mai Deng said in a statement that the general's arrest "violates" the 2018 power-sharing agreement that ended five years of civil war.

"This act puts the entire agreement at risk," the statement said.

"We are also gravely concerned about the heavy deployment of SSPDF around (Machar's) residence," it added.

The UN Mission in South Sudan last month reported increased fighting between the army and "armed youth" in Nassir, Upper Nile state, involving "heavy weaponry which has, reportedly, resulted in deaths and injuries to civilians as well as armed personnel".

The 2018 peace deal ended a civil war fuelled by the rivalry between Kiir and Machar. Some 400,000 people died in the conflict.

The war came just two years after South Sudan became independent from Sudan. The country remains mired in poverty and violence.