They are all thought to be lorry drivers from Bulgaria, Greece, Turkey and Lithuania, Greek authorities said.
Firefighters have spent a second day tackling the flames and the continuing fire has hampered rescue attempts but the ship has been towed closer to land.
A total of 280 people were evacuated and two airlifted from the ferry after being trapped in the hold.
The Euroferry Olympia, owned by Italian firm Grimaldi Lines, had left Igoumenitsa in Greece for the Italian port of Brindisi when the fire broke out on a car deck.
The ferry was officially carrying 239 passengers and 51 crew, according to the company. But two Afghan nationals who were not registered as passengers on the ship were also rescued on Friday, the Greek coastguard told AFP news agency.
Image source, EPA
Firefighters continued to tackle the blaze for hours on Saturday
Dozens of people rescued from the ferry have been taken to a hotel on Corfu. One of them, lorry driver Danilo Carlucci, told Reuters: “We saw death in front of us.”
The cause of the fire remains unknown but the Greek coastguard told Reuters a prosecutor had ordered an inquiry into the incident, adding the captain and two first mates had been briefly detained to testify before being released.
Authorities will have more evidence about the cause of the fire once the fire is out and the ship can be tugged to a safe place, Shipping Minister Giannis Plakiotakis told Greek television. He said when the fire was out, fuel would be pumped out in an attempt to avoid marine pollution.
But AFP reported the Italian environment ministry said a “possible spill” had been detected by an Italian coastguard air crew.
Image source, Reuters
Evacuations began minutes after the fire started
A specialised Greek rescue team was able to board the vessel more than 12 hours after the fire broke out, but smoke has continued to billow from the ferry on Saturday as strong winds rekindled the fire.
Authorities have given details about the 12 people missing, saying they are likely to be lorry drivers. Seven are from Bulgaria, three are from Greece, one is from Turkey and one is from Lithuania.