The European Union formally issued a warning Friday to Greece to reportedly fix serious oversights along its borders or face a suspension from the border-free Schengen zone for up to two years. The troubled country will now have three months to fix its borders as thousands of refugees continue to stream to its shores on their way to other European countries.

Greece has "seriously neglected" its obligations to control the external frontier of Europe's passport-free Schengen zone, the European Commission had said in January in its draft report. The assessment reportedly found failures to register, check and fingerprint migrants arriving in November.

According to a source cited by Reuters, the commission gave Athens 50 recommendations to tighten border checks. With a very limited timeframe to achieve them, a lapse by Greece could trigger an unprecedented activation of rules allowing member states to reimpose controls on internal Schengen frontiers for up to two years.

While European policy makers maintained that the move is not intended to isolate or stigmatize Greece but rather to ensure that border controls elsewhere in Europe, including between Germany and Austria, can remain in place, the Greek government lashed out at what it called EU's "blame games." Athens opposed the move in the EU ministerial council Friday.

Several EU members such as Austria and Hungary have already introduced temporary border controls, as passport-free travel in Schengen zone comes under increased strain.