General Andre Kinkela, the Congolese army commander in eastern Ituri district, was quoted as saying that "the two sides must remain in permanent contact and collaborate closely to peacefully solve any problems that could come up instead of resorting to armed force".
Armed men killed a British oil contractor on Friday in a pre-dawn raid on a boat operated in Ugandan waters by Canada's Heritage Oil Corp, and a Congolese soldier was killed in an exchange of fire with Ugandan forces later the same day.
Uganda's General Hudson Mukasa blamed the recent incidents on poor demarcation of the border by former colonial powers Britain and Belgium.
"We hope that political officials of the two governments will talk about it and find a solution," he said.
Relations between the two Great Lakes neighbours have been strained since Congo's 1998-2003 war, in which Uganda-backed rebels tried to overthrow the Congolese government.
Ugandan troops occupied parts of Congo during the five-year conflict and are accused of pillaging natural resources in territory under their control.
Lake Albert, one of several lakes on East Africa's Great Rift Valley, possibly lies above reservoirs of crude oil. Both Congo and Uganda hope to benefit if oil is found beneath the lake bed.