An explosion at a fuel depot wounded more than 200 people, according to Armenian separatist authorities AFP

Envoys from Baku and Yerevan prepared to meet in Brussels for talks on Tuesday as thousands of refugees fled Nagorno-Karabakh after Azerbaijan's lightning takeover of the majority ethnic Armenian enclave.

Last week, an offensive by Baku's forces established Azerbaijani control over the breakaway region, forcing ethnic Armenian fighters to disarm.

Tuesday's meeting in Brussels will be the first such encounter since the offensive but the leaders of both countries are scheduled to meet next month.

Simon Mordue, chief diplomatic adviser to European Council president Charles Michel, will chair the talks, Michel's spokeswoman said.

Azerbaijan and Armenia, along with EU heavyweights France and Germany, will be represented by their national security advisers.

Several days after the fighting, the first refugees arrived in Armenia on Sunday and 6,650 people have so far entered, Yerevan said on Monday.

AFP reporters saw the refugees crowding into a humanitarian hub set up in a local theatre in the city of Goris to register for transport and housing.

"We lived through terrible days," said Anabel Ghulasyan, 41, from the village of Rev, known as Shalva in Azeri.

She arrived in Goris with her family by minibus, carrying her belongings in bags.

An explosion at a fuel depot wounded more than 200 people, according to Armenian separatist authorities which have been supplying those seeking to leave the territory with petrol and diesel.

"As a result of the explosion in the fuel warehouse, the number of injured exceeds 200. The health condition of the majority is severe or extremely severe," the region's rights ombudsman Gegham Stepanyan said on social media.

"The medical capacities of (Nagorno-Karabakh) are not enough," he added, calling for air ambulances to be allowed to land.

An official had earlier indicated there were fatalities, without giving a toll.

Armenia and Azerbaijan have fought two wars in the last three decades over Nagorno-Karabakh, a majority ethnic Armenian enclave within the internationally recognised border of Azerbaijan.

Azerbaijan's lightning operation on September 19 to seize control of the territory forced the separatists to lay down their arms under the terms of a ceasefire agreed the following day.

It followed a nine-month blockade of the region by Baku that caused shortages of key supplies.

The separatists have said 200 people were killed in last week's fighting.

Baku announced two of its soldiers also died when a mine hit their vehicle on Sunday.

Azerbaijan's state media said officials held a second round of peace talks with Nagorno-Karabakh's ethnic Armenian community aimed at "reintegrating" them.

But on the road heading to Armenia, more and more residents from the region appeared to be trying to get out as witnesses said cars were snarling up in traffic.

"Who would have thought that the 'Turks' would come to this historic Armenian village? It's incredible," she said, referring to the Azerbaijani forces.

She was being housed temporarily in a hotel in Goris and had "nowhere to go".