About 100 U.S. special forces helping with intelligence and logistical support also called off operations temporarily, a U.S. embassy official said, but it was not immediately clear if troops from other countries in the regional force were also giving up the search.
Kony is wanted by the International Criminal Court for war crimes. He and his commanders are accused of abducting thousands of children to use as fighters in a rebel army that earned a reputation for chopping off limbs as a form of discipline.
Uganda provides more than 3,000 troops of a 5,000-strong African Union force hunting Kony and his fighters, thought to be hiding in jungles straddling the borders of Central African Republic, South Sudan and Democratic Republic of Congo.
A separate coalition of rebels in Central African Republic, known as Seleka, toppled President Francois Bozize last month. They swept into the capital Bangui in a lightning offensive which triggered days of looting and drew international condemnation.
The Seleka rebels also killed 13 South African soldiers during their attack on Bangui.
"These rebels have been openly hostile to us and following that, the president (of Uganda, Yoweri Museveni) has ordered us only to be in defensive positions," said Dick Olum, head of Ugandan troops in the force hunting Kony and also the overall force commander.
"So we've temporarily suspended offensive operations against the LRA for now until we receive further orders," he told Reuters on Wednesday.
Crane Elise, U.S. embassy information officer in Kampala, said U.S. special forces had "temporarily paused the operations against LRA to give us time to consult with our partners."