Tajikistan and Kyrgyzstan said Friday they had agreed a ceasefire after shootouts at their contested border left two Tajik citizens dead.

The violence that broke out Thursday evening and continued into the night was the bloodiest escalation between the countries since deadly clashes last year.

Kyrgyz and Tajik frontier communities regularly clash over land and water supplies, with border guards often drawn into the conflicts.

As a result of the latest conflict, "10 people were injured on the Tajik side, of which six were servicemen and four were civilians," Tajikistan's national security committee said.

Tajikistan added that the two dead were a man "killed by a mortar shell fired by Kyrgyz soldiers into his yard" and an ambulance driver.

Following the overnight clashes, Kyrgyzstan's national security committee said Friday that it had reached an agreement for "a complete ceasefire" with Tajikistan during a meeting at the border between provincial governors and border service representatives.

The neighbours also agreed to withdraw forces, coordinate patrols of the frontier and ensure the flow of traffic along a strategic road that passes between both countries.

Kyrgyz President Sadyr Japarov sought to reassure citizens the conflict would be resolved "peacefully, through negotiations, God willing".

"Do not believe the false information spread for the purpose of escalating the situation by individual media and politicians who pursue interests of other countries," Japarov said on Facebook.

Tajikistan, an authoritarian country, confirmed the agreement several hours later.

"At present, the situation on the state border of Tajikistan and Kyrgyzstan is stable, the causes and factors of the border conflict are being studied by a joint commission of the relevant structures of both parties," the Tajik national security committee said.

As is custom during border flare-ups between Central Asia's two poorest countries, the narrative as to how the latest clashes in the remote area began was fiercely contested.

Kyrgyz border guards patrol the contested frontier with Tajikistan
Kyrgyz border guards patrol the contested frontier with Tajikistan AFP / VYACHESLAV OSELEDKO

Kyrgyzstan's national security committee accused Tajik troops of "using mortars and grenade launchers" in the exchanges that the committee said began just after 7:30 pm Kyrgyzstan time (1330 GMT) on Thursday.

The shooting started almost immediately after the sides had agreed to reopen a road blocked by Tajik citizens, the committee added.

Tajikistan's national security committee said that tensions had arisen after a group of Kyrgyz nationals "forcibly stopped" a Tajik vehicle transporting sand between two Tajik villages at around 1220 GMT.

Kyrgyz authorities then failed to show for a meeting with Tajik officials called to "prevent such illegal incidents", the committee claimed.

"Instead, Kyrgyz border guards, who had taken up firing positions along the perimeter of (a bridge) opened fire on civilians of the Republic of Tajikistan", the committee added, complaining that "flights of drones, violating the airspace of the Republic of Tajikistan, were observed."

Tajikistan also accused Kyrgyzstan of distributing false information "in order to hide its illegal actions".

Kyrgyzstan accused Tajikistan of distorting information. "It was Tajik border guards who have recently used (drones) for reconnaissance purposes".

"It is concerning that instead of strengthening the Tajik-Afghan section of its border, where there is an accumulation of about 8,000 militants of terrorist organisations, the Tajik side is determined to escalate conflicts on the Kyrgyz-Tajik border," Kyrgyzstan's national security committee said.

Kyrgyzstan's health ministry said at least 11 of its citizens were being treated for moderately serious injuries.

Asia Plus, a private Tajik news agency, reported that as many as 17 Tajiks had been injured.

Close to 1,500 Kyrgyz citizens were evacuated from villages near where the conflict took place at the intersection of Tajikistan's northern Sughd province and Kyrgyzstan's southwestern Batken province, the emergencies ministry said.

Last year's violence between the two militaries was unprecedented, leaving more than 50 people dead.

Almost half of the pair's 970-kilometre-long(600-mile) border is disputed and progress on delimitation in recent years has been glacial.