Ugandan and American troops have suspended their joint hunt for war crimes suspect Joseph Kony and his Lord’s Resistance Army, delivering a major setback to efforts to capture a notorious warlord accused of abducting tens of thousands of children.

The Ugandan military and the U.S. State Department separately announced Wednesday that they had temporarily halted the search because of political turmoil in the Central African Republic, where Kony and his deputies are thought to be hiding.

Rebel groups unaffiliated with Kony seized power in the Central African Republic last week, forcing President Francois Bozize — who had been friendly with Washington — to flee the country.

Col. Felix Kulayigye, a Ugandan army spokesman, told reporters that the hunt for Kony would remain on hold “until further notice” because rebel leaders in the Central African Republic were refusing to cooperate with Ugandan troops stationed in the country.

Shortly afterward, State Department officials in Washington said the U.S. military would likewise “pause” its operations in the Central African Republic. A Pentagon spokesman said that about 40 U.S. Special Forces troops are deployed in the country, where they are advising and training about 3,000 African troops — mainly Ugandans — looking for Kony in the jungle.

Lord's Resistance Army area of influence

President Obama deployed about 100 U.S. Special Forces troops to Africa in October 2011 to coordinate a regional effort to track Kony, a brutal and messianic Ugandan guerrilla leader who has been on the run for a quarter-century.

The U.S. military said it will not withdraw its troops from the Central African Republic for now in hopes that a political solution can be reached soon so the search for Kony can resume. Meanwhile, the 40 U.S. Special Forces troops will remain at two camps deep in the bush, near the towns of Obo and Djema.

The rest of the 60 U.S. troops are stationed in Uganda, South Sudan and Congo, where they will continue normal operations, said Maj. Robert Firman, a Pentagon spokesman.

Kony and most of his deputies are thought to be hiding in the Central African Republic, but they regularly cross borders and are well-practiced at disappearing into the bush. They long ago stopped using radios and cellphones to avoid leaving an electronic trail, frustrating U.S. efforts to track them with satellites and surveillance aircraft.

The suspension of the search overshadowed a previously planned announcement Wednesday by the State Department to offer $5 million in rewards for information leading to the arrest or conviction of Kony or two other LRA leaders, Okot Odhiambo and Dominic Ongwen.

Donald Y. Yamamoto, the State Department’s acting top diplomat for African affairs, said the U.S. government “remains very committed” to defeating the LRA. “Even though we’ve taken a pause because of the developments” in the Central African Republic, he told reporters, “we’re going to use all facilities and all technology at our hands to try to find and locate Kony and his crew.”

Kony created the Lord’s Resistance Army in the 1980s to overthrow Uganda’s government. The militia left Uganda several years ago but continued to terrorize villagers in central Africa across a swath of terrain the size of California, kidnapping children and transforming them into killers and sex slaves.

Over the past two years, the militia has significantly weakened, numbering no more than a few hundred fighters, according to U.N. officials and analysts. High-profile defections have fragmented the group, which now stages assaults mostly for food and supplies.

But the announcement Wednesday has raised fears among international human rights groups that Kony and the LRA could regroup and reignite their campaign of brutality.

“A premature withdrawal would have devastating and immediate consequences for civilians in LRA-affected areas,” said Ben Keesey, head of Invisible Children, an activist group that prominently raised public awareness about the LRA’s atrocities last year. “It gives Kony a new lease on life, enabling him to regain power by initiating new rounds of abductions in communities that will be left totally unprotected and vulnerable to LRA attacks.”

The Ugandan military also is not planning to remove its soldiers from the Central African Republic, Kulayigye said, but it will confine them to their bases until the African Union clarifies their status. The African Union has suspended the membership of the Central African Republic and imposed travel restrictions on the rebels who have appointed themselves leaders of the country.

Kulayigye also warned that Kony and the LRA could use the suspension of the search as an opportunity to stage attacks.

Bozize, the ousted leader of the Central African Republic, also had seized power in a coup. But he welcomed the presence of the Ugandans and the Americans and their efforts to eliminate Kony and the LRA.

The International Criminal Court at The Hague has indicted Kony on 33 counts of war crimes and crimes against humanity, including murder and rape.

Last year, Invisible Children released the short film “Kony 2012,” which generated more than 100 million views online, bringing global attention to the LRA.

Whitlock reported from Washington.