Greek authorities had earlier quarantined the Ritsona camp in central Greece after 20 asylum seekers tested positive for coronavirus.
Greece has quarantined a second migrant facility this week after a 53-year-old man tested positive for coronavirus, the migration ministry said on Sunday.
The Afghan man, who was found to be infected, lives with his family at the Malakasa camp along with hundreds of other migrants and asylum seekers.
He has been transferred to a hospital in Athens. Tests on his contacts will continue as the public health agency tries to trace the route of the virus.
On Thursday, authorities quarantined the Ritsona camp in central Greece after 20 asylum seekers tested positive for coronavirus.
It was the first such facility in Greece to be hit since the outbreak of the disease.
The camp in Malakasa, 40km (25 miles) northeast of Athens, will be put into quarantine for two weeks, the ministry said, adding that police guarding the site would be reinforced.
A new separate closed-type facility started operating last month for migrants who arrived after March 1, the ministry said.