Museveni was speaking to the United Nations Secretary General, Antonio Guterres at the sidelines of the 30th African Union Heads of State summit happening in Addis Ababa, Ethiopia.
The two discussed issues of peace and stability in the Great Lakes Region and the reforms being undertaken by the United Nations, especially on the peacekeeping front.
On the question of achieving peace and stability in South Sudan, President Museveni reiterated his position that leadership legitimacy must be derived from the people, saying the country must organise elections.
“It is the population which can hold leaders accountable. They should hold elections for this to happen,” said Mr Museveni.
On his part, Mr Guterres said he would rally the international community to offer more support to the African peacekeeping mission in Somalia, AMISOM, and also briefed the President on efforts underway to reform UN peacekeeping missions.
“We want the peace missions to be more agile, more effective with better intelligence and better movement,” said the secretary general. “We must also have an exit strategy for our missions.”
President Museveni advised that the reforms should emphasize the need for the missions to work closely with the communities they serve.
He also counseled that the UN reforms should try and address the question of “ideological leukemia”, which sometimes has seen the UN end up supporting “sterile political opportunists”.
The two leaders also agreed that they would follow up on pledges made during the Refugee Solidarity Summit in Kampala last June to ensure they are fulfilled and host communities supported.
Similarly, the president of the Democratic Republic of Congo Joseph Kabila has confirmed his country will hold elections.
He said polling will go ahead, even though voting has already been postponed twice.
He also denied accusations that his security forces are cracking down on protesters who are calling for him to step down.
Kabila held a rare press conference in an apparent response to international condemnation of the violent treatment of Catholic Church members and activists protesting his prolonged stay in power. On Friday, Joseph Kabila called on the Central African country's electoral process "firmly engaged" that despite a long-delayed vote, his country was not for sale.
Congolese security forces killed at least six people and injured 68 others on Sunday as thousands of demonstrators held nationwide protests calling for Kabila, whose mandate ended in late 2016, to step down.
The United Nations says excessive force was used.
The UN this week also blamed Congolese "state agents" for 1 176 extrajudicial killings last year.
Kabila criticized the UN for its slow humanitarian
Nearly 7 000 Congolese have crossed Lake Tanganyika and taken refuge in Burundi since the clashes raged between DRC government forces and rebels in the troubled eastern province of South Kivu.
Burundi police said a total of 6 692 people had registered as refugees to escape fighting between the army and the Yakutumba militia, although the flow appeared to have since slowed.
The DRC government last week announced it was waging "war" against two militias in the east - the Yakutumba and the Ugandan Islamist rebels of the Allied Democratic Force (ADF).
The ADF are active in North Kivu while the Congolese Yakutumba are several hundreds of kilometres away in South Kivu. Both regions border Uganda, Rwanda, Burundi and Tanzania.
Rival militia groups have long held sway over large areas in the two provinces, often competing for their rich mineral resources.
Meanwhile, the office of the U.N. High Commissioner for Human Rights is urging Government of Democratic Republic of Congo to investigate the alleged killings by security forces during anti-government protests. The Human Rights office warns the latest crackdown by security forces in DRC saying it indicates a recurring pattern of repression against political opponents of Congolese President.