Prime Minister Alexis Tsipras on Friday admitted Greek border controls had been overwhelmed by the mass arrival of refugees earlier this year, but insisted all migrants were now being properly documented.
His defence came after the European Commision this week launched legal procedures against Croatia, Greece and Italy for failing to register all migrants in the EU-wide fingerprint database, Eurodac, when they first arrive on the continent.
Tsipras told lawmakers the government had initially been "taken by surprise" by the sheer number of migrants, "but since September there has not been a single arrival who has not been registered."
Registering new arrivals would help with security, as national police forces and Europol can compare fingerprints linked to criminal investigations with those in Eurodac.
Tsipras however said that due to a lack of equipment, fingerprinting migrants and registering the data took "several hours."
The Eurodac Regulation calls for fingerprinting asylum seekers and filing the data within 72 hours.
Tsipras said European countries had to pitch in with more equipment. The foreign ministry said Friday only 39 biometric machines had been provided against 100 demanded.
After revelations that two jihadists involved in the Paris terror attacks slipped into Europe through a Greek island, posing as refugees, Athens has faced heavy scrutiny over its screening of more than 750,000 people who have landed on its shores this year.
Greece on Thursday said it would seek to deport economic migrants, who had been blocked at its border with Macedonia after Skopje clamped down on entry, if they are not entitled to asylum.
"Those without papers, the so-called illegal migrants, have the right to request asylum (or) the right to voluntary repatriation," junior interior minister for migration Yiannis Mouzalas told reporters.
"If they do not request either within 30 days, they will be returned to their countries of origin," he said.