The spokesman for joint Congolese-Ugandan military operations, Lieutenant-Colonel Mak Hazukay, told reporters that the shooting occurred on a highway linking Beni to the northeastern town of Kasindi in eastern DRC's Rwenzori region.
A Ugandan private "inadvertently fired ... on two of his comrades" on Tuesday morning, Hazukay said, without offering further details of the incident.
One Congolese soldier and one Ugandan soldier were killed, he added. The perpetrator is under arrest.
Ugandan troops first entered the DRC in late November to combat the Allied Democratic Forces (ADF) militia.
Initially limited to the DRC's eastern North Kivu province, the Ugandan military operation expanded to neighbouring Ituri province in late January.
The Congolese and Ugandan armies are trying to guard the Beni-Kasindi highway, where a Ugandan company is carrying out construction work under an agreement between the two neighbours.
Claimed by the Islamic State group as its Central African offshoot, the ADF has been accused of massacring thousands of Congolese civilians and carrying out terrorist attacks in neighbouring Uganda.
ADF massacres have continued despite joint operations between Ugandan and Congolese troops. The militia is one of more than 120 armed groups active in conflict-torn eastern DRC.