BRUSSELS (AP) — A European Union investigation found major flaws in Greece's border management that could pave the way for other EU nations to isolate Athens and 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 its 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."

The government in Athens has three months to fix the problems.

More than 850,000 people are thought to have entered Greece last year seeking sanctuary or jobs in Europe but 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. EU nations would have to vote in favor of the move by around a two-thirds majority, but Greece alone could not stop them.

Any failure in the next few weeks to come up with a new mechanism allowing the border controls could see the whole Schengen border region unravel.

"Schengen is one of the most formidable achievements of the European Union and it must be protected," Commission Vice President Valdis Dombrovskis told reporters.

Greece is certainly under pressure. Already its EU partners have dispatched dozens of officers to Macedonia to help police the Greece-Macedonia land border.

"I am uneasy because there is an effort to create an atmosphere against Greece," Greek Migration Minister Ioannis Mouzalas told private Skai television. But he conceded "it's a bad report for us and it documents something that is true."

Mouzalas said things have already improved since the inspections late last year.

"Our commitment now is to be ready by mid-to-late February," he said.

Derek Gatopoulos in Athens contributed.