The withdrawal came Wednesday after the self-proclaimed president of the Central African Republic, Michel Djotodia, called on all foreign troops to leave the country, The Wall Street Journal reported.
Djotodia took over after a rebel overthrow of the the government last month. The suspension of Uganda's search for Kony in the Central African Republic signals the country could descend into greater chaos after the overthrow, the newspaper said.
Kony is the leader of the Lord's Resistance Army, notorious for kidnappings, killings and forced enlistment of children in its ranks.
After Uganda's withdrawal Wednesday, the United States announced a $5 million bounty for information leading to Kony's capture. The U.S. government added the warlord to a list of wanted war criminals, The Wall Street Journal reported.