A European Union investigation has found major flaws in Greece's management of its borders, which could pave the way for its EU partners to introduce long-term ID checks to restrict the entry of migrants further into the continent.

Backing up the suspicions of several EU nations, surprise inspections by expert teams in Greece, including on Aegean islands near the coast of Turkey, found that Greek authorities were failing to properly register and fingerprint people or correctly check their travel papers.

The EU's top migration official, Dimitris Avramopoulos, said Wednesday that their "report shows that there are serious deficiencies in the management of the external border in Greece."

More than 850,000 people are thought to have entered Greece last year seeking sanctuary or jobs in Europe. Greece only has shelter for about 10,000 people. The Greek coast guard is simply overwhelmed, and thousands of migrants have moved north, hoping to find a home in wealthy EU countries like Germany or Sweden.

The report is important because Germany has temporarily reintroduced border controls in its part of the passport-free Schengen area until May 13 after around 1 million people applied for asylum in Germany last year. Beyond that date, Berlin has no legal means of maintaining ID checks.

But if the EU's executive Commission rules that Greece has demonstrated "serious deficiencies in carrying out external border control," countries like Germany, Austria and Sweden could possibly keep their border controls on for up to two years.

The report's wording of "serious deficiencies" is a sign that this will happen in the near future. EU nations would have to vote in favor of the move by around a two-thirds majority, but Greece alone could not stop them.

In response to Europe's worst immigration emergency since World War II, nations have erected razor-wire fences, deployed troops and tightened border controls. So far, most steps have respected the letter, if not the spirit, of the Schengen rule book.

But any failure in the next few weeks to come up with a new mechanism allowing controls could see the Schengen border code unravel.