Tajikistan's President Emomali Rahmon has ordered troops and police to cease fire in the town of Khorog in Tajikstan's restive Gorno-Badakhshan region, with authorities starting talks with militants after gun battles have left at least 40 dead, a local official said on Wednesday.

At least 30 militants were killed with another 40 arrested on Tuesday during a special operation against an armed group believed to be linked to the murder of a senior Tajik security official. Twelve Tajik security officers were killed and another 25 injured during the operation.

The armed group is led by local opposition strongman Tolib Ayombekov, reports say. Local security official Abdullo Nazarov was stabbed to death on Saturday.

Security forces say they decided to use force after Ayombekov refused to surrender.

Ayombekov was a member of the opposition which fought against the government during Tajikistan's civil war in the 1990s.

The operation is yet another attempt by the Tajik government, which has little influence in the area, to bring Gorno-Badakhshan under its full control. However, it remains a base for former rebel fighters.

A former Soviet republic, Tajikistan plunged into civil war almost as soon as it became independent from the Soviet Union in 1991. It is Central Asia's poorest nation.

"The ceasefire would allow us to search for wounded and clear the streets of decomposing bodies," Governor of Badakhshan region, Kodiri Kosim, said at a meeting with local residents. , RIA Novosti reported.

A special commission comprising leaders of the local community will be set up to determine if there were civilian casualties during the clashes.

Tajik authorities on Wednesday started talks with representatives of the militant group led by local warlord Tolib Ayombekov, which has been involved in drug smuggling and has also carried out a series of killings in the mountainous region bordering with Afghanistan.

The group is believed to be behind the murder of Maj. Gen. Abdullo Nazarov, chief of the Tajikistan National Security Committee regional office, on June 21.

His car was stopped by a group of unidentified persons several kilometers from Khorog, he was pulled out of the car and stabbed several times. The general died on the way to hospital.

Tajik opposition sources are reporting hundreds of civilian casualties and claim that Nazarov's murder, and the recent attacks on government officials, have been used by Tajik authorities as a pretext for an ethnic cleansing campaign, and an attempt to reestablish control over the region which has long been known as a fiefdom of local warlords.