Armenia said on Saturday that over 100,000 people have fled Nagorno-Karabakh, meaning nearly all the official population of the ethnic Armenian enclave has left since Azerbaijan seized back control.

Nazeli Baghdasaryan, a spokeswoman for Armenia's prime minister, said the number of refugees entering the country over the past week had reached 100,417.

The exodus comes after the Armenian enclave – estimated before to have a population of 120,000 – saw its decades-long fight against Azerbaijani rule end in sudden defeat.

Baku reconquered the territory – internationally recognised as part of Azerbaijan – in a lightning offensive last week that appeared to bring the curtain down on the festering conflict.

The ethnic Armenian authorities in the self-proclaimed republic announced it was officially ceasing to exist after they agreed to capitulate and hand over their arms.

Artak Beglaryan, a former separatist official, said that according to unofficial information "the last groups" of Nagorno-Karabakh residents were on their way to Armenia on Saturday.

"At most a few hundred persons remain, most of whom are officials, emergency services employees, volunteers, some persons with special needs," he wrote on social media.

The flood of humanity across the border into Armenia in the past few days has rewritten a centuries-old ethnic makeup of the disputed region.

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

But Baku has denied the claim and has publicly called on the Armenian residents of the territory to stay and "reintegrate" into Azerbaijan.

The United Nations will send a mission to Nagorno-Karabakh this weekend, mainly to assess humanitarian needs, UN spokesman Stephane Dujarric announced, adding that the body had not had access to the region "in about 30 years."

Armenia has asked the UN's highest court to take urgent measures to protect the enclave's inhabitants, the court announced on Friday.

Yerevan urged the International Court of Justice (ICJ) to ensure that Azerbaijan doesn't move to displace the remaining ethnic Armenians in Nagorno-Karabakh or prevent "the safe and expeditious return" of those who have already fled.

The International Federation of Red Cross and Red Crescent Societies on Friday announced an emergency appeal for 20 million Swiss Francs (US$22 million) to help those fleeing. (AFP)