"He [Zuma] arrived this afternoon at 2pm and is currently locked up in a meeting with the president," Okello Oryem, Uganda's minister of state for foreign affairs in charge of international affairs, told The Anadolu Agency.
"They are discussing regional issues to do with peace and security," he said.
Among topics to be addressed by the two African leaders are efforts by the Intergovernmental Authority on Development (IGAD), a regional grouping, to bring peace to war-torn South Sudan.
"President Zuma wants to see how South Africa can help using the spirit of the African National Congress," said Oryem.
South Sudan descended into chaos one year ago following a power struggle within the ruling Sudan People's Liberation Movement.
The conflict has claimed tens of thousands of lives, displaced nearly two million people and left about four million people at risk of food insecurity, according to humanitarian agencies.
Presidents Museveni and Zuma will also discuss the repatriation of M23 rebels to their native Democratic Republic of Congo.
Last week, over 1,000 M23 rebels fled from a camp in Western Uganda to avoid being forcefully repatriated to another country.
M23 spokesperson Kabasha Amani told AA at the time that one year after signing the Nairobi agreement, the amnesty process had been hindered by the government of President Joseph Kabila.
He said the government had not implemented the agreed measures regarding security or the modality of disarmament, cantonment, demobilization and the social reintegration of M23 fighters.
Minister Oryem also said the two presidents would discuss a pending deadline presented to the Congo-based Rwandan Democratic Forces for the Liberation of Rwanda (FDLR).
Countries in the region had given the Rwandan rebels a six-month deadline, which expires on January 2, to lay down their arms or face military action.
In August, the UN Security Council asked the East African Joint Force to prepare for an offensive if the rebel group did not surrender and renounce violence.
Last month, a local daily in Uganda reported that FDLR leader Victor Byiringiro, in a letter dated November 3, expressed his readiness to send group fighters to a collection center designed by the United Nations Organization Stabilization Mission in the Democratic Republic of the Congo (MONUSCO).
While the M23 is reportedly supported by Uganda and Rwanda, a claim denied by both countries, the FDLR is also reportedly supported and armed by Tanzania and South Africa.
The FDLR consists of Hutu fighters and families that fled Rwanda after the Rwanda Patriotic Front, led by President Paul Kagame, took over the country in 1994.
Disarming the FDLR, of which only 1,500 combatants remain, took on added urgency following the defeat of the mainly Tutsi M23 rebels in the eastern DRC late last year.
FDLR military commander Sylvestre Mudacumura is wanted by the International Criminal Court for war crimes, including torture, in connection with a murderous rampage in North and South Kivu in 2009 and 2010.
Two FDLR leaders, Ignace Murwanashyaka and his deputy, Straton Musoni, stood trial in Germany in 2011 on charges of mass killings and rape.
The two face 26 counts of crimes against humanity and 39 counts of war crimes.