Uganda and the US have ended a six-year hunt for the fugitive warlord Joseph Kony, the leader of the Lord’s Resistance Army.

But the conclusion of the mission has frustrated the commander of Ugandan forces in Central African Republic, where the search has focused, and left advocacy groups concerned that the failure to “kill or capture” Kony could allow the LRA to rise again.

Uganda began withdrawing its troops from their base in eastern CAR last week. The departure of 100 US special forces, who worked alongside the Ugandan soldiers, began this week.

The mission, known as the African Union Regional Taskforce, was a wholly Ugandan affair almost from the start.

It was supposed to have been 5,000-strong, drawing troops from South Sudan, the Democratic Republic of the Congo and CAR. But the neighbouring countries, with security problems of their own, either never deployed or quickly withdrew their contingents.

The taskforce failed to win donor funding, and Uganda ended up footing the bill. Since 2011, armed US special forces advisers have provided intelligence and logistics support.

Colonel Richard Otto is the commander of Uganda’s contingent in CAR. At his divisional headquarters in Uganda’s northern city of Gulu, the former senior military intelligence officer explained the difficulty of his three-year posting.

“In CAR, the area we are operating in is almost the size of Uganda. You can imagine [the vastness], and I don’t have enough troops.”

The taskforce was drawn from all units of the Ugandan army, but may not have exceeded 1,500 men, according to media reports.

CAR has been the perfect hideaway for the LRA. It has been convulsed by violence since 2013, when a predominantly Muslim coalition of rebels known as the Séléka overthrew the government. The UN mission, Minusca, has been unable to end ongoing violence between Christian militia and the former Séléka.

“The armed forces of CAR are yet to be organised,” said Otto, who before his deployment in CAR served as chief operations planner with African Union forces in Somalia.

“Some of them are undergoing training by [the] UN [and the] European Union Training Mission, and they are not yet deployed in the eastern part of the country.”

The lawlessness of CAR has attracted not only Séléka from neighbouring Chad, but also other armed men including the Janjaweed militia from Sudan’s Darfur region, who have crossed the border to poach elephants.

“We have quite a number of armed groups,” said Otto. “So, when you encounter them in the jungle, sometimes it’s difficult to know whether you are fighting LRA or other [forces].”

But the Ugandan troops have recorded significant successes. Four key LRA commanders have been captured, and an insurgency of 2,000 fighters that terrorised a huge swath of territory across central Africa has been sharply degraded.

The LRA, now believed to be down to less than 120 armed men, has splintered into small units operating in the remotest regions of eastern CAR, north-eastern Congo, and Darfur.

“The enemy is permanently on the run,” said Otto, claiming that there had been a steady trickle of defections and more than 1,000 civilians abducted by the LRA had been rescued.

Kony, wanted by the international criminal court for war crimes and crimes against humanity, has a $5m (£3.9m) bounty on his head. He is believed to be hiding in the Kafia Kingi enclave, a disputed border area between Sudan and South Sudan.

Khartoum is not a member of the regional taskforce and, as a historical supporter of the LRA, appears to have given Kony safe haven.

Members of Uganda’s Lord’s Resistance Army, pictured in 2006. Photograph: AP

Crucially, though, he no longer leads his men. “He has lost command, control, and communication,” said Otto. “For the first time, the LRA has factions. There is a group … who has decided to leave [the] LRA and operates on [its] own.”

Two senior LRA commanders, Bosco Kilama and Peter Ochora, who defected last month in Congo, agree with Otto’s assessment on the group’s disintegration.

“The LRA is disarray. The LRA has been completely disorganised with no central command. Kony is growing old and losing the grip on the soldiers,” Kilama told reporters at Uganda’s Entebbe airbase last week. The two men will receive a government amnesty.

The LRA’s apparent toothlesness has allowed the Ugandan army and the US Africa Command to trumpet Kony’s irrelevance as justification for their withdrawal from the hunt.

But Otto, an Acholi from northern Uganda, the original heartland of the LRA, acknowledges that the group remains a threat.

“The will to fight and attack the security forces is not there. However, they still remain a problem to the general population,” he said.

“They are involved in looting food, looting gold, diamonds, killing elephants in [Congo’s] Garamba national park and Zemongo national park in CAR,” he said. It is a revenue stream that could keep them armed for years.

The LRA was responsible for 563 abductions in 171 attacks in 2016, according to the LRA Crisis Tracker, a monitoring group. It’s a drop from the 737 people kidnapped in 2015 in 222 attacks, but still significant.

As of 30 March this year, they are believed to have kidnapped 147 people in 43 incidents.

“Completely abandoning the mission will create security vacuums for already extremely vulnerable communities, particularly in the Central African Republic and north-eastern DRC,” said Holly Dranginis, a senior analyst at the US-based Enough project.

“Leaving now will also dismantle key defection sites, leaving individuals with scarce options if they want to leave the LRA and reintegrate into civilian life,” she said.

Lino Owor Ogora, director of the Gulu-based Foundation for Justice and Development Initiatives, noted: “The LRA has always taken advantage of any lapses in combat to regroup and reorganise.

“People in northern Uganda have enjoyed peace for close to 10 years now, and the region is on a firm road to recovery. It would be unfortunate if the LRA returned because they were allowed to.”

There is also unease in CAR. On 16 April, civilians demonstrated in Obbo town, which has been the tactical headquarters for Ugandan and US forces, calling for the troops to stay.

Otto is now back in CAR finalising the return home of the last of his men.

But the Ugandan government has hinted that it will not step away altogether from an insurgency that began in Uganda almost three decades ago, and was then exported to its neighbours.

Richard Karemire, the military spokesman, said last week that Uganda could join the UN peacekeeping mission in CAR under a strengthened mandate to tackle the LRA.

Joseph Kony, pictured in 2006. Photograph: Stringer/AFP/Getty Images

He also suggested Uganda could support “capacity-building” of the Central African Armed Forces for “counter-LRA operations”.

Ogora also favours a military option, drawing on the UN and regional armies to “neutralise” the LRA once and for all.

“Short of that, the LRA will continue roaming the jungles of Garamba at will, trading in ivory and arms, and abducting and killing civilians.”

But Phil Clark, a Great Lakes expert at Soas University of London, says the military option has been tried and has failed. “This requires a political solution, with amnesty at its core,” he said.

According to Dranginis, “the United States should continue supporting defection campaigns”, which have proved successful in “weakening the group and creating opportunities for fighters and abductees to leave”.

Demobilisation and reintegration is a complex process, she added, but it “can pay dividends for security in the region”.