Uganda's parliament endorsed Tuesday the government's decision to send troops to neighbouring war-ravaged South Sudan, with the defence minister saying the army had help avert "genocide".

Ugandan troops deployed in South Sudan five days after fighting began last month, both to support President Salva Kiir and to help evacuate its citizens.

"That a genocide was looming in South Sudan was a reality," Defence Minister Crispus Kiyonga told parliament.

"The army in South Sudan is split. One side is on the rebels' side and another on the government side."

However, the initial decision to send troops across the border was made without approval of parliament, sparking criticisms from some lawmakers and prompting a special sitting of the house on Tuesday.

"We all agree the decision to deploy troops, though without approval of parliament, was a right one considering the humanitarian reasons as explained by government," parliament speaker Rebecca Kadaga said.

No announcement was made as to how many -- and for how long -- troops would be deployed.

However, the defence minister said the military will have a mandate to evacuate citizens, "protect the trade route between us and South Sudan as well as engage in peace enforcement" while "maintaining neutrality" as the two sides negotiate.

Opposition leader Wafula Oguttu said sending troops had been the right decision, but that he had opposed "activities that bring to question our neutrality".

Uganda, whose border lies less than 100 kilometres (miles) from Juba, is a major trading partner for the world's newest state.

Ugandan President Yoweri Museveni last month warned rebel chief Riek Machar to sign a ceasefire or face action by regional nations.

Over 40,000 South Sudanese refugees have fled into Uganda since fighting broke out on December 15. Up to 10,000 people are believed to have been killed in the fighting, aid sources and analysts say.