Uganda's army will leave neighbouring South Sudan by next month, the head of the country's armed forces said Monday.

"The boys are coming home. We will be out by the first week of November," General Katumba Wamala told reporters in the capital Kampala.

Uganda's President Yoweri Museveni deployed troops to South Sudan in support of President Salva Kiir in his 21-month long war with rebels led by former deputy president Riek Machar.

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

Last year the United Nations accused the Uganda People's Defence Force (UPDF) of using outlawed cluster munitions in South Sudan, a charge denied by Uganda.

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 at the weekend, but that deadline was missed.

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

James Mugume, a senior foreign ministry official, said the Ugandan withdrawal would begin at once.

"Uganda has with immediate effect from today started to pull out of South Sudan," he said.

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.