Greek Cypriots voted overwhelmingly against a UN plan for reunification on Saturday, scuttling plans to bring them together with their Turkish neighbours ahead of entry into the European Union.

Turkish Cypriots from the poorer northern half of the island voted to support the plan, which needed the approval of both communities.

Only the Greek portion of the island will enter the EU on May 1.

Turkish Cypriots voted 64.9 per cent in favour of the plan even though they would have lost territory, while Greeks were 76 per cent opposed.

The European Commission said it "deeply regrets that the Greek Cypriot community" had rejected the plan.

"A unique opportunity to bring about a solution to the long-lasting Cyprus issue has been missed," the commission said in a statement from Brussels.

Some 643,000 Greek Cypriots live in the southern half of the island, while 180,000 Turks and Turkish Cypriots inhabit the northern half, where Islam is the dominant religion.

The UN plan called for a federation of two politically equal states under a weak central government -- an idea that angered both sides.

The plan would also have reduced the Turkish area of the island from 37 per cent to 29 per cent, requiring whole villages to be uprooted and returned to their original Greek Cypriot owners.

The 40,000 Turkish and 6,000 Greek foreign troops would have seen their numbers gradually reduced by more than 75 per cent by the year 2018.

Some Turkish Cypriots saw acceptance of the plan as a pathway to greater prosperity.

However, Rauf Denktash, leader of the breakaway north, was opposed, calling the plan an "extermination" of Turkish Cypriots.

"If both sides say yes, we shall continue to struggle about all the points of which we are still in disagreement," he said.

In the south, Greeks complained the plan limited the right of refugees to return to homes they fled after Turkey invaded the north three decades ago.

While there are many sources of conflict between Turkish and Greek Cypriots, one thing keeping them apart has been the presence of Canadian troops.

But some argue that has created complacency and reduced political will to hammer out a solution.

There is disagreement on that idea.

"All Greek-Cypriots and all Turkish-Cypriots want a unified Cyprus but the plan is simply too flawed in the eyes of most people," said Lou Mitsis of the B.C. Cypriot Association.

With a report from CTV's Todd Battis