As uncertainty looms over the refugee deal between the European Union and Turkey, Greek judges ruled that a Syrian asylum-seeker should not be sent to Turkey, terming the country unsafe, according to reports Friday. Amnesty International said the decision might put the EU-Turkey deal in peril.

The Syrian, who arrived on the Aegean island of Lesbos in Greece, had appealed against the rejection of his asylum application. A committee that decides on matters related to rejected asylum applications ruled that the refugee should not be sent to Turkey calling it an “unsafe country,” Greek newspaper Kathimerini reported Friday.

However, a source at the Greek migration ministry told BBC that the judges were only deciding whether the Syrian national’s case could be heard in Greece.

Earlier in the day, Greek and EU officials sent back 51 refugees to Turkey from Lesbos and Kos islands of Greece, under the EU-Turkey deal that came into force in March. Since March, over 400 asylum-seekers, who crossed the Aegean Sea to Greece, have been sent back to Turkey.

Greece Turkey refugees number EU Deal Refugees queue for food at a makeshift camp along the Greek-Macedonian border, April 20, 2016. Photo: Getty Images/AFP/Daniel Mihailescu

Under the deal, Ankara will get visa waiver to Schengen zone if it agrees to take back refugees who arrived in Greece through Turkey. The visa-free travel to the Schengen Area for Turkish citizens will depend on the country’s compliance with all 72 conditions that the EU has outlined. These requirements range from respect for human rights to biometric passports.

Amnesty spokesman Giorgos Kosmopoulos told BBC that Turkey, at present, does not protect asylum-seekers under the Refugee Convention and that there had been “widespread returns of Syrians back to Syria from Turkey.” He noted that refugees in Turkey could not expect access to the rights to work, medical care or family life.

“Until it becomes a safe country nobody should be returned there,” Kosmopoulos said. "The whole [EU] deal should stop and refugees should be settled in other European countries safely and with dignity."

The EU-Turkey deal was signed on March 18 to tackle the worst refugee crisis in Europe in decades that has seen over a million people from Syria, Afghanistan and elsewhere pass through European borders.