Azerbaijan has detained the former president of Nagorno-Karabakh "on suspicion of waging an aggressive war" and alleged war crimes, the prosecutor general and security service said in a joint statement on Thursday.
Arayik Harutyunyan, 49, stepped down shortly before Baku's lightning offensive to retake the disputed region, which was under the control of ethnic Armenian forces.
He led the separatist government during the 2020 armed conflict between Baku and Yerevan for control of the mountainous enclave and stepped down in early September, shortly before Baku's offensive.
Several senior representatives of Karabakh's former authorities and military command have also been detained, including Ruben Vardanyan, a reported billionaire who headed the region's separatist government between November 2022 and February 2023.
Armenia's foreign ministry said on Wednesday it "strongly condemned" Azerbaijan for the arrests, adding that it "will take all possible steps to protect the rights of the illegally arrested representatives of Nagorno-Karabakh, including in international courts".
Separatist authorities in the breakaway region agreed to disarm, dissolve their government and reintegrate with Azerbaijan after Baku's one-day military operation in late September.
The central government in Baku is holding re-integration talks with separatist leaders, but Azerbaijan's Prosecutor General Kamran Aliyev has said criminal investigations had been initiated into crimes committed by 300 separatist officials.
The United Nations human rights office has urged Baku to afford the detainees "full respect and protection".
Nagorno-Karabakh, which is internationally recognised as part of Azerbaijan, first came under the control of ethnic Armenian forces backed by the Armenian military in separatist fighting that ended in 1994.
Azerbaijan retook parts of the area in a war in 2020.
But after last month’s defeat, separatist authorities surrendered their weapons and held talks with Azerbaijan on reintegration of the territory into Azerbaijan.
Most ethnic-Armenian residents – more than 100,000 people – have since fled.
Earlier this month, Hikmet Hajiyev, a diplomatic adviser to Azerbaijani President Ilham Aliyev, said it had detained "five to six" people whom it accused of war crimes but said that people leaving the country were doing so of their own free will.
"They are free. If somebody puts down his gun, they are free and they have decided on their own choice to go to the republic of Armenia," he said.
"If they accept Azerbaijan citizenship, we will protect and ensure their rights and their security, and we will establish a municipality system so that they can govern their affairs at a local level, and religious and cultural rights will be assured."
Thousands flee Nagorno-Karabakh - in pictures
