Some Ugandan forces were killed and wounded, Museveni said, in a clash with rebel troops a day before the Ugandan parliament approved their deployment, the Sudan Tribune reported Thursday.
The Ugandan army had denied any involvement in the fighting.
Addressing heads of state Wednesday at a conference in Angola, Museveni said the Ugandan casualties occurred in a clash Monday with the forces of ousted South Sudan vice president Riek Machar about 55 miles outside of South Sudan's capital Juba.
He said Ugandan forces "inflicted a big loss on the side of the rebels. We also took casualties and had some dead."
Machar claimed Tuesday his forces defeated a combined South Sudan-Uganda force backed by helicopter gunships, dozens of tanks and other heavy artillery.
He has denounced the involvement of Ugandan troops and made their withdrawal from the country a condition for a cease-fire.
The Obama administration on Wednesday confirmed the Ugandan's army involvement in the conflict.
Linda Thomas-Greenfield, assistant U.S. secretary of state for African Affairs, told a congressional hearing Uganda wanted to protect certain structures vital to the flow of goods and people between Uganda and the Juba airport.
"They indicated they have an interest in a stable South Sudan but also said they have an interest in ensuring that a democratically elected government is not overturned by violent means," she said in response to a question by Rep. Randy Weber, R-Texas.