Uganda's army has begun its pull-out from neighbouring South Sudan, in line with a peace deal aimed at ending nearly two years of civil war, an official said Tuesday.

Uganda's President Yoweri Museveni deployed troops to South Sudan in support of President Salva Kiir, who is fighting rebels led by former deputy president Riek Machar.

The Ugandan soldiers have played a key role in defending the capital Juba and have used helicopter gunships to fend off rebel attacks elsewhere in the country.

As part of a peace deal mediated by regional bloc IGAD and signed in Addis Ababa in August by Kiir and Machar, the Ugandan soldiers were supposed to leave South Sudan earlier this month.

"There is an agreement between the government of South Sudan and the government of Uganda that the UPDF (Uganda People's Defence Force) withdraw from South Sudan back to Uganda," South Sudan government spokesman Michael Makuei told AFP.

"This process has started today," he added, explaining that Ugandan troops in Bor, a key town north of Juba, were moving south to the capital where they would link up with other UPDF troops and then leave the country.

"It is a force with a lot of equipment and lot of things that need to be assembled, need to be organised," he added, hinting the process would not be quick.

The demilitarisation of government-held Juba to allow the return of Machar and his rebel entourage is a key provision of the peace agreement.

The Ugandan soldiers are due to be replaced by a neutral force, while South Sudanese soldiers are to be relocated to barracks outside the city.