Ongoing clashes between South Sudan government forces and rebels will be the key item on the agenda as African Union leaders meet in Kigali on Sunday. The Burundi crisis is also to be addressed.
On Friday, relative calm had returned to South Sudan's capital Juba but the UN has warned of the likelihood of fresh fighting amid rising tension. The UN mission in South Sudan (UNMISS) said it is evacuating all its non-essential staff following reports that government troops were targeting UN staff and foreign aid workers.
"The reports include allegations of the killing of at least one South Sudanese national working for an international NGO, as well as rapes, including of international NGO staff. UN staff members have also been assaulted," UN spokesman Stephane Dujarric said.
The recent violence in Juba which claimed more than 200 lives and displaced 40,000 is a huge blow to the AU's aim of bringing peace to the continent by 2020. "What has happened in South Sudan is totally unacceptable," said Nkosazana Dlamini-Zuma, the outgoing AU chairperson. She called on the leaders, President Salva Kiir and his deputy Riek Machar, to protect their people and not be the cause for their suffering.
South Sudan's crisis was triggered in December 2013 by a political battle between Kiir and Machar. A peace deal signed in August by the two leaders to end the civil war is now in doubt after the latest violence.
Divisions over who should head the AU Commission could complicate any efforts to bring peace to South Sudan. The three main contenders, Botswana's Foreign Minister Pelonomi Venson-Moitoi, her Guinean compatriot Agapito Mba Mokuy and Uganda's former vice president Specioza Wandira-Kazibwe, have all been described as "lacking stature" by several African countries.
If none of them wins outright, the vote could be postponed until January 2017 at the next AU summit in Addis Ababa. According to the AU Commission spokesman Jacob Enoh Eben, the Commission is ready for the crucial vote. "There are rumors, but it's up to the heads of state to decide if they want to vote or not," Enoh Eben said.
Another important item on the agenda for the African Union will be to seek a lasting solution to the Burundian crisis. Hundreds of people have been killed since President Pierre Nkurunziza stated he would run for a third controversial term in April 2015.
Several top military officers have been targeted including Hafsa Mossi, a former Burundian government minister for East African Community Affairs, who was shot dead on Wednesday by unknown gunmen.
So far, all efforts to end the crisis have borne little fruit, with the government shunning the latest effort in Tanzania attended by opposition and civil society members.
The Burundian government has consistently rejected suggestions by the AU to deploy 5,000 peacekeeping troops, saying it will prevent such a force from crossing its borders.
Sudan's Bashir: welcomed but also wanted
Rwanda has insisted that Sudan's President Omar al-Bashir is "very welcome" to attend the AU summit in Kigali. Bashir is wanted by the International Criminal Court (ICC) to answer charges of war crimes, crimes against humanity and genocide allegedly committed in the restive Darfur region. 300,000 people have been killed in Darfur, according to the UN.
Rwanda's top envoy, Louise Mushikiwabo, told reporters that her nation has no obligation and no right to arrest anybody.
Rwanda is not a signatory of the Rome Statute which founded the ICC. Mushikiwabo also dismissed a request by the ICC to arrest Bashir should he set foot in Rwanda. "We are too busy to pay attention to that kind of thing," she said. Mushikiwabo referred to the ICC request as a "distraction."
"Anybody who is invited by the African Union will be here in Kigali and would be very welcome and would be under the protection of this country as should be customary," Mushikiwabo added. African leaders have become increasingly critical of the ICC, accusing it of targeting countries in Africa while turning a blind eye to western countries.