The Celtic wide man was injured during Greece's 2-1 win in Latvia on Friday.
Although he was only on the park for 22 minutes, he suffered ligament damage on an elbow.
He will return to Glasgow today for more tests to see if he has suffered any lasting damage.
But he is a certainty to miss at least the start of Celtic's Champions League campaign.
A Greek FA spokesman said: "Samaras will return to Scotland. He has had an initial scan which showed he has suffered an outside collateral ligament rupture and no bone damage.
"His condition will be reassessed today to see if he requires surgery. If he doesn't require an operation, he will be missing for four to five weeks. If he does, it could be longer.
"Our doctors will keep in constant touch with Celtic's doctors to monitor his condition."
Samaras' representatives were angry with the Greeks for playing him because he had a back problem anyway.