Police are investigating the cause of the fire. There were no casualties.
The government has constructed a temporary camp in a military base by the sea full of hundreds of canvas tents.
Authorities said some 300 people have entered the camp until now, but many migrants refuse to enter, calling it another 'Moria' and saying movement would be restricted by police.
Greece and the European Union said last week a new modern camp with better standards will replace Moria, but migrants have staged two protests asking European states to take them in.
Migrants entering the tent camp are tested for coronavirus, and a special quarantined area has been set up for positive cases.
Concerns were raised when 35 positive cases from Moria went missing during the fire.
Officials said on Sunday (September 13) seven people that entered the camp have tested positive. The camp will be closed at night and guarded by police.