Azerbaijan said Wednesday it had regained control over breakaway Nagorno-Karabakh for the first time in decades after separatist Armenian fighters agreed to lay down their arms in the face of a military operation.

The stunning collapse of separatist resistance represents a major victory for Azerbaijan President Ilham Aliyev in his quest to bring the Armenian-majority Nagorno-Karabakh back under Baku's control.

Armenia and Azerbaijan have fought two wars over the mountainous region since the collapse of the Soviet Union.

The years of conflict have been marked by abuses on both sides, and there are concerns of a fresh refugee crisis as Karabakh's Armenian population fears being forced out.

A day after Azerbaijan launched its military operation in the region, Baku and the ethnic Armenian authorities in Karabakh announced a ceasefire deal had been brokered by Russian peacekeepers to stop the fighting.

"Azerbaijan restored its sovereignty as a result of successful anti-terrorist measures in Karabakh," Aliyev said in a televised address.

Aliyev claimed that most of the Armenian forces in the region had been destroyed and said the withdrawal of separatist troops had already begun.

The attack left "at least 200 killed and more than 400 wounded," Nagorno-Karabakh separatist official Gegham Stepanyan said.

Late on Wednesday, Armenia's defence ministry said that Azerbaijan had fired on its positions along the border between the arch-foes. Such skirmishes are frequent along the border.

Truce deal

Under the truce deal, the separatists said they had agreed to fully dismantle their army and that Armenia would pull out any forces it had in the region.

Azerbaijan's defence ministry said that "all weapons and heavy armaments are to be surrendered" under the supervision of Russia's 2,000-strong peacekeeping force on the ground.

Both sides said talks on reintegrating the breakaway territory into the rest of Azerbaijan would be held on Thursday in the city of Yevlakh.

President Vladimir Putin said Russian peacekeepers would mediate the talks.

Moscow has said several of members of its force in Karabakh were killed when the car they were travelling in came under fire.

Latest violence

Baku's operation marked the latest violence over the rugged territory.

After the Soviet Union fell apart, Armenian separatists seized the region — internationally recognised as part of Azerbaijan — in the early 1990s.

The war left 30,000 people dead and forced hundreds of thousands from their homes.

In a six-week war in 2020, Azerbaijan recaptured swathes of territory in and around the region.

President Aliyev on Wednesday praised the "political competence" of his country's historic rival.

"The developments that took place yesterday and today will have a positive impact on the peace process between Azerbaijan and Armenia," he said.

Azerbaijani presidential foreign policy advisor Hikmet Hajiyev promised safe passage for the separatists who surrendered and said Baku sought the "peaceful reintegration" of Karabakh Armenians.

A separatist official said over 10,000 people have been evacuated from Armenian communities in Nagorno-Karabakh and "forced to find a shelter" elsewhere in the territory.

Russia's President Putin said he hoped for a "peaceful" resolution, adding that Moscow has been in contact with all sides in the conflict.

Putin held talks with Armenian Prime Minister Nikol Pashinyan Wednesday evening, but the Kremlin insisted the crisis was "Azerbaijan's internal affair".

'War is over'

Jubilant residents in Azerbaijan's capital expressed hope the deal heralded a definitive victory and the end of the decades-long conflict.

"I was very happy with this news. Finally, the war is over," 67-year-old pensioner Rana Ahmedova told AFP.

In Armenia, there was fury at a second defeat in Karabakh in three years.

Clashes broke out in Armenia's capital Yerevan, where thousands of protesters waving the separatist region's flag blocked a main road and riot police guarded official buildings.

Demonstrators threw bottles and stones at police as they slammed the government's handling of the crisis, while officers used stun grenades and made arrests.

The loss in Karabakh ratchets up domestic pressure on Pashinyan, who has faced stinging criticism at home for making concessions to Azerbaijan since the 2020 defeat.

"We are losing our homeland, we are losing our people," said Sargis Hayats, a 20-year-old musician.

Pashinyan "must leave, time has shown that he cannot rule. No one gave him a mandate for Karabakh to capitulate," he said.

The Armenian leader has insisted that his government had not been involved in drafting the latest ceasefire deal.

Again denying his country's army was in the enclave, he said he expected Russia's peacekeepers to ensure Karabakh's ethnic-Armenian residents could stay "in their homes, on their land".

International pressure

Azerbaijan's assault came as Moscow, the traditional power broker in the region is bogged down and distracted by its war on Ukraine, which has left it isolated in the West.

But its peacekeepers there appeared to have played a key role in helping to negotiate the ceasefire and will now oversee its implementation.

Turkey, a historic ally of predominantly Muslim Azerbaijan that views mostly Christian Armenia as one of its main regional rivals, had called the operation "justified".

The EU and United States have been mediating talks between Baku and Yerevan in recent months aimed at securing a lasting peace deal between the two foes.

The White House said Wednesday it was concerned by the humanitarian situation in Nagorno-Karabakh.

"We're obviously still watching very, very closely the worsening humanitarian situation inside Nagorno-Karabakh," US National Security Council spokesman John Kirby told reporters.

He added the situation "has been exacerbated by the hostilities perpetrated by Azerbaijan" in Karabakh, where there are now fears of a refugee crisis.