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Armenian separatist officials in Nagorno-Karabakh said Monday they would stay in the breakaway region following Azerbaijan's offensive to retrieve the victims of fighting and a deadly fuel depot blast.

Armenia separatists say over 200 people were killed in fighting with Azerbaijan late last month and that a further 170 died when a fuel depot exploded as scores of civilians fled Karabakh over fears of ethnic cleansing.

After three decades of Armenian control, the separatist authorities have agreed to disarm, dissolve their government and reintegrate with Azerbaijan in the wake of Baku's one-day military operation in late September.

The separatist government said President Samvel Shahramanyan will stay in Karabakh's main city of Stepanakert with a group of officials "until the search and rescue operations for the remainder of those killed and those missing" are completed.

"The government continues to focus on the issue of those citizens who want to move to the Republic of Armenia," the government added in a statement.

Separatist official Artak Beglaryan said "a few hundred" Armenian representatives remained in Karabakh.

He said they included "officials, emergency service, volunteers, some persons with special needs."

Most of Karabakh's estimated 120,000 residents have fled the territory.

"Despite strong words, Western countries have limited scope for action in Nagorno-Karabakh."

Unpacking the geopolitical implications of Nagorno-Karabakh's demise👇

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Yerevan has accused Azerbaijan of conducting a campaign of "ethnic cleansing" to clear Karabakh of its Armenian population.

Baku has denied the claim and called on Armenian residents of the territory to stay and "re-integrate" into Azerbaijan, saying their rights would be guaranteed.

AFP journalists on Monday saw a convoy carrying water and communications workers that was allowed to enter Stepanakert.

The convoy was escorted by the Azerbaijani army.

They also saw a bus carrying officials who planned to open a "re-integration" office in the city for any ethnic Armenians wishing to register with Azerbaijani authorities.

Azerbaijan is holding "re-integration" talks with separatist leaders.

Several senior representatives of its former government and military command have been detained.

Azerbaijan's Prosecutor General Kamran Aliyev said criminal investigations had been initiated into war crimes committed by 300 separatist officials.

"I urge those persons to surrender voluntarily," he told journalists on Sunday.