Yoweri Museveni, who backed South Sudan's now-ruling SPLM in its decades-long conflict with Sudan before independence in 2011, sent his troops across the border at Juba's invitation shortly after fighting began in mid-December last year.
Since then, Uganda's military presence has been a bone of contention during drawn-out peace talks in the Ethiopian capital between President Salva Kiir and rebels led by his sacked ex-deputy Riek Machar.
Machar has demanded Uganda's urgent withdrawal.
"The problem is not with Uganda. The problem is peace among (South) Sudanese, and in order to not leave a vacuum we agreed that other IGAD countries should deploy and now they are deploying," Museveni said in a press conference, referring to east Africa's IGAD bloc, which is mediating the talks.
"I think Ethiopian forces are already there (in South Sudan), and Rwanda is there. Once they are ready, and can ensure that at least Juba is not affected ... then we shall go back. There is no big issue."
Fierce fighting erupted in the country last December, two years after Juba declared independence from Khartoum, following months of tension between Kiir and Machar.
The United Nations says the civil war has killed more than 10,000 people, caused over a million to flee and driven the country of 11 million towards famine.
Regional efforts led by neighbouring Ethiopia to find a peaceful solution to the conflict have made limited gains amid bouts of fighting, despite Kiir and Machar signing a ceasefire in January and then again in May.
The warring parties re-committed to stop fighting and bring their conflict to an end without conditions in November, but sporadic bouts of fighting resumed swiftly after the latest agreement.
Both Ethiopia and Uganda have also contributed troops to an African peacekeeping mission in war-torn Somalia, which has remained in the grip of violence since 1991.
In 2011, the two countries signed a regional security operations deal that provides for both states to take common position on regional security affairs.
The agreement was also meant to allow for free movements of people between the two countries.