Story highlights

At least 42 people are killed in fighting

Tensions run high in the area; ethnic Pamiris have been at odds with the government

The region was a stronghold for Islamist rebels during a bloody civil war

The standoff began in late July

CNN  — 

Tolib Ayombekov, a former opposition warlord believed to have been behind the killing of a top security general, surrendered to Tajik authorities early Tuesday, ending a three-week standoff, a government spokesman said.

In a statement aired on Badakhshan TV, Ayombekov said he turned himself in to end the violence in Khorog, Pamir – the capital of the Gorno-Badakshan region in eastern Tajikistan.

More than 40 people were killed and many residents were displaced in recent fighting. Also communications with the outside world have been virtually severed during the fighting between Ayombekov’s forces and government troops.

The cutoff of communications began Tuesday, when fighting erupted in the autonomous region – also known as Pamir – after central government forces attempted to arrest a former opposition warlord believed to have been behind the killing of a top security general.

The government accuses Ayombekov’s fighters in last weekend’s killing of Maj. Gen. Abdullo Nazarov, head of the regional branch of the State Committee on National Security, which is a successor to the Soviet KGB.

In that incident, a group of unidentified people stopped Nazarov’s car near Khorog, according to Ria-Novosti, a Russian state-run news service. He was pulled from the car, stabbed several times and died en route to a hospital, according to Ria-Novosti.

A spokesman for the government in the Tajik capital of Dushanbe said the killing was “the last straw.” He said the warlords were troublemakers.

In his last public appearance before he went into hiding early this week, Ayombekov told reporters that Nazarov’s security detail had failed to protect him. It was not clear what he meant by that.

Ayombekov is the suspected leader of a ring that smuggled tobacco, precious jewels and drugs, the Central Asian News Service said.

Until last week, Ayombekov had been working for Nazarov overseeing border security between Tajikistan and Afghanistan, an administration official in Badakhshan told CNN. The official did not want to be identified because he is not allowed to speak to the news media.

Tajikistan gained independence with the collapse of the Soviet Union in 1991 but has been troubled ever since by bloody war, widespread corruption and poverty.

Read more: Clinton discusses human rights, regional security in Tajikistan

Tensions remain high between the Tajik government in Dushanbe and the people of Gorno-Badakshan, who are of the Pamiri ethnic minority.

The region was a stronghold of Islamist rebels during a five-year civil war in the 1990s that claimed thousand of lives. The war also divided people along ethnic and regional lines, and the Pamiris, by and large, sided with the opposition.

A United Nations-brokered peace plan left President Emomali Rakhmon’s secular government in place but gave some of his Islamist opponents official jobs.

But Rakhmon, backed by Moscow, has sought to consolidate power and stamp out remnants of radical Islam.

Khorog residents said they received no warning of Tuesday’s fighting. People panicked as gunfire rang out.