"We confirm that the Syrian passport holder came through the Greek island of Leros on October 3 where he was registered under EU rules," said a statement issued by Nikos Toskas, the minister for citizen protection.
French police said the document was found "near the body of one of the attackers" in the investigation into the main attack of yesterday's carnage, at the Bataclan concert hall, where 82 people were killed.
European security officials had long feared that jihadists could take advantage of the mass migration influx, mainly from war-torn Syria, that Europe has been experiencing since the beginning of the year.
A Greek police source on Saturday said Athens had forwarded to French authorities the fingerprints of the passport holder registered on Leros in October, to check whether he was actually involved in Friday's attacks.
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Greece's junior minister for migration Yiannis Mouzalas had admitted in September that it would be "foolish" to completely discount the possibility of jihadists sneaking into Europe among the refugee wave.
But Mouzalas noted that the number of Europeans joining extremist groups in the Middle East was far higher.
"The opposite is happening. They leave from here and go over there," he said.
Prime Minister Alexis Tsipras on Saturday insisted that the refugees fleeing Syria "are hunted by the same terrorists" that struck in Paris yesterday.
"We must find solutions to the drama of the people who leave their homes, hunted by the same terrorists, and drown in the Mediterranean," Tsipras said in a televised address.