Armenia was due to hand over disputed territory to Azerbaijan on Friday as part of a contentious Russian-brokered peace accord that ended weeks of brutal fighting over the Nagorno-Karabakh region.

The Armenian residents of Azerbaijan's Aghdam district hurriedly picked pomegranates and persimmons from trees surrounding their homes and packed vans with furniture, AFP journalists said, before fleeing before the official deadline to cede the mountainous province.

Armenian soldiers
Armenian soldiers and residents were pulling out of Aghdam district before a deadline as part of a peace deal Photo: AFP / Karen MINASYAN

"We wanted to build a sauna, kitchen. But now I had to dismantle everything. And I'll burn down the house with everything I own when I leave," Gagik Grigoryan, a 40-year-old electrical worker, told AFP before abandoning his home.

Columns of tanks and troop transporters filled with waving Armenian fighters rolled out of the territory through dense fog ahead of Friday's deadline to vacate the region.

Nagorno-Karabakh map
Map locating the disputed region of Nagorno-Karabakh with zones of control. Photo: AFP / Jonathan WALTER

Fierce clashes between Azerbaijan's forces and Armenian separatists broke out in late September in the Nagorno-Karabakh region. The brutal war lasted six weeks, leaving thousands dead and displacing many more.

The longstanding ex-Soviet rivals finally agreed to end hostilities last week under the framework of a Russian-brokered accord that sees Moscow deploy peacekeepers to the region and requires Armenia to cede swathes of territory.

Separatists in Nagorno-Karabakh and several surrounding districts captured the territory and claimed independence that has not been recognised internationally, even by Armenia, following a post-Soviet 1990s war that left some 30,000 dead.

Armenian residents of Aghdam
Armenian residents of Aghdam rushed to leave before the deadline to cede the mountainous province back to Azerbaijan Photo: AFP / Andrey BORODULIN

As part of last week's peace deal, Armenia agreed to return some 15 to 20 percent of the Nagorno-Karabakh territory captured by Azerbaijan in recent fighting, including the historical town of Shusha.

The exchange of territory was originally due to begin Sunday, with Armenians in the Kalbajar district fleeing en masse before the official deadline for Azerbaijan's takeover.

Armenian refugees
A truck carries a barn as Armenian refugees leave the village of Nor Maragha near Agdam Photo: AFP / Andrey BORODULIN

But Azerbaijan's President Ilham Aliyev postponed the deadline by one week over "humanitarian" considerations.

Armenians
IMAGESThe Armenians heave freshly-slaughtered pigs into the back of a van as they rush to pack every single one of their possessions before Azerbaijani forces arrive. As the village of Nor Maragha empties, even an entire house is loaded onto a flatbed truck so the incoming Azerbaijanis have nothing left to recover. Photo: AFPTV / Andrey BORODULIN

In addition to Friday's deadline to cede Aghdam, Armenia will hand over the Kalbajar district wedged between Nagorno-Karabakh and Armenia on November 25 and the Lachin district by December 1.

The Russian peacekeeping force of some 2,000 troops has deployed to the administrative centre of the region, Stepanakert, and set up checkpoints and observation posts along the strategic Lachin corridor connecting Nagorno-Karabakh with Armenia.

While Armenians in the provinces to be handed over to Azerbaijan have left in an exodus, the Russian mission on Thursday said it had bussed some 3,000 residents back to Stepanakert and other regions who had fled during the six weeks of heavy shelling.

Most of Azerbaijan's south-western district of Aghdam has been under the control of Armenian separatists since 1993. Before the post-Soviet war it was inhabited by some 130,000 people -- mostly ethnic Azerbaijanis who were expelled from their homes.

Armenia's health ministry said earlier this week that more than 2,400 of the country's fighters had been killed in the fighting. Azerbaijan has not revealed its military fatalities.

After the peace accord was signed last week, Russian President Vladimir Putin said total fatalities that include dozens of civilians had surpassed 4,000 people.

Russia's decisive role in the settlement has sidelined international players the United States and France, which brokered a ceasefire in the 1990s but failed to deliver a long-term resolution.

During the most recent conflict, France, the United States and Russia attempted to broker three separate ceasefires that collapsed as Armenia and Azerbaijan accused the other of violations.

French President Emmanuel Macron this week urged Russia to clarify "ambiguities" over the Moscow-brokered ceasefire, including Turkey's role in the peacekeeping mission.

Azerbaijan has insisted on a prominent role for its staunch ally Turkey, which was widely accused by Western countries, Russia and Armenia of supplying Baku with mercenary fighters from Syria over the weeks of fighting.

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