Azerbaijan said on Sunday it had agreed to extend a deadline for Armenia to withdraw from a disputed district as part of a peace accord that ended six weeks of fierce fighting over the Nagorno-Karabakh region.

The first of the territories, Kalbajar, was to be turned over on Sunday. But Azerbaijan agreed at the last minute to give Armenian forces and civilians until November 25 to withdraw.

Kalbajar is home to the well-known Dadivank monastery of the Armenian Apostolic Church. On Saturday, a day before the territory’s expected handover, workers removed many of the monastery’s sacred objects.

Azerbaijani presidential spokesman Hikmet Hajiyev said on Sunday that the delay was requested by Armenia and granted “taking into account the worsening weather conditions and the difficult mountainous terrain".

“Kalbajar's settlement by Armenians was illegal. The people who were resettled there have no property rights,” Hajieyv told a news conference.

Kalbajar was almost exclusively populated by ethnic Azerbaijanis before they were expelled by Armenians in the 1990s war between the two countries over Nagorno-Karabakh, and a majority of the homes being abandoned previously belonged to Azerbaijanis.

Residents of the Kalbajar district in Azerbaijan that was controlled by Armenian separatists for decades began a mass exodus of the mountainous province in the days leading up to the official withdrawal day.

Civilians fleeing the region caused huge traffic jams on the single road leading to Armenia. AFP journalists saw fleeing residents pile furniture and kitchenware into vehicles before leaving for Armenia and some among the departing ethnic-Armenians said they had exhumed graves they feared would be desecrated by Azerbaijanis.

Thick plumes of smoke were rising over the valley near the village of Charektar after residents set their homes on fire preferring to leave devastation in their wake and homes that would be uninhabitable by Azerbaijanis.

“We also moved our parents' graves, the Azerbaijanis will take great pleasure in desecrating our graves. It's unbearable," one Charektar resident said.

A Russian peacekeeping contingent deployed this week to Nagorno-Karabakh.

They set up checkpoints and positions in the region's administrative centre, Stepanakert, as part of the terms of the accord that sees Armenia cede swathes of territory that Azerbaijan's forces gained in the fighting.

Moscow's peacekeeping mission, which the military said included soldiers that previously were stationed in Syria, comprises some 2,000 troops for a renewable five-year mission.

The ex-Soviet rivals agreed to end hostilities earlier this week after efforts by Russia, France and the United States to get a ceasefire fell through during the nearly two months of clashes.

A key part of the peace deal includes Armenia's return of Kalbajar, as well as the Aghdam district by November 20 and the Lachin district by December 1, which have been held by Armenians since a devastating war in the 1990s.

Azerbaijan vows to protect Christian churches

Meanwhile, the president of Azerbaijan promised that Christian churches will be protected when the Muslim-majority country takes possession of areas formerly controlled by Armenians.

President Ilham Aliyev’s office said he made the promise in a telephone call with Russian President Vladimir Putin, who is deploying peacekeeping forces in the areas under an agreement that ended six weeks of fighting between Armenia and Azerbaijan over the Nagorno-Karabakh region.

Azerbaijan is about 95 per cent Muslim and Armenians fear that churches would be damaged or closed when it takes control of the territories.

“President Aliyev said that Christian churches in Azerbaijani territories, which are returned to Azerbaijan in accordance with the trilateral statement, will also be properly protected by the state. Christians of Azerbaijan will have access to these churches,” said the statement from his office.

Outrage over peace deal

Armenia conceded on Saturday that 2,317 fighters were killed in clashes in which both sides accused the other of targeting civilian infrastructure.

Azerbaijan has not revealed its military casualties and the real toll after weeks of fighting is expected to be much higher.

Russian President Vladimir Putin on Friday said the number of fatalities had surpassed 4,000 and that tens of thousands of people had been forced to flee their homes.

Before departing en masse, Armenians flocked to the Dadivank monastery nestled in a gorge in Kalbajar for a final visit before it was ceded to Azerbaijan, with AFP journalists witnessing a dozen women ask to be baptised at the religious site.

Kalbajar was almost exclusively populated by ethnic Azerbaijanis before they were expelled by Armenians in the 1990s war following the breakup of the Soviet Union, and a majority of the homes being abandoned previously belonged to Azerbaijanis.

The Armenian government controversially subsidised the region's settlement by ethnic Armenians.

The peace accord with Azerbaijan has sparked a week of protests in Armenia where demonstrations and opposition parties are calling for Prime Minister Nikol Pashinyan to resign.

The former head of Armenia's national security service Artur Vanetsyan was arrested on Saturday on charges of plotting to kill Pashinyan and seize power.

Azerbaijan has pushed for Ankara's involvement in the settlement and Turkish President Recep Tayyip Erdogan said this week his country would jointly supervise the ceasefire with Russia.

Turkey, a key ally of Azerbaijan, was widely accused by Western countries, Russia and Armenia of dispatching mercenaries from Syria to reinforce Azerbaijan's army.

But Russia has ruled out Ankara's direct involvement in the peacekeeping mission and instead insisted Turkey would instead monitor the mission from an observation centre on Azerbaijan's territory.