A huge police operation in Macedonia ensured a partial re-run of parliamentary elections on Sunday passed peacefully after the European Union warned that the country's membership bid was on the line.

Police special forces secured polling stations in dozens of ethnic Albanian towns and villages as the authorities clamped down to prevent a repeat of the fraud, intimidation and gunfights that marred the original June 1 election.

The results of the re-run, involving around 10 percent of the population, cannot alter the overwhelming victory of Prime Minister Nikola Gruevski's conservative VMRO-DPMNE.

But its conduct could be crucial with the EU weighing whether to open accession talks with Macedonia later this year, a move cast into doubt by the violence of two weeks ago.

Foreign election monitors will issue initial findings on Monday. But Macedonian authorities said voting had gone smoothly, with the exception of "minor irregularities."

"The state electoral commission has evaluated the electoral process so far as positive and correct," commission president Jovan Josifovski told reporters shortly before polls closed.

Police said there had been "no reports of the use of firearms or any violence at the electoral posts."

Macedonia's 25 percent Albanian minority is split between two rival parties vying for control of the north and west of the country, and a place in Gruevski's likely coalition government.

Gruevski had echoed appeals for calm from the EU and the United States, and warned party activists and their "political mentors" that he would not tolerate a repeat performance of the violence in which one person was shot dead.

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Gruevski's conservatives won the healthiest parliamentary majority in more than a decade, riding a wave of nationalist sentiment after Greece in April blocked an invitation for Macedonia to join NATO in a row over the country's name.

The EU is determined to keep the former Yugoslav republic on the path to membership, to tackle the unemployment and poverty that continue to fuel tensions seven years after an Albanian guerrilla insurgency tipped Macedonia to the brink of civil war.

NATO and EU diplomacy persuaded the guerrillas to disarm and enter politics, in exchange for greater rights. But reform has been slow.

Monitors said the original election had fallen short of international standards, accusing the government of contributing to an atmosphere of impunity after it failed to prevent violence.

"Trouble brings no good to anyone, but that was the past and we hope for better now," said voter Ilaz Prkopuca in the former militant stronghold of Aracinovo. A second man blamed bad governance for the violence.

"The Macedonian leadership is not heading in the right direction, and that's why we have a re-run," said Naser Jakupi.

The election violence was not ethnically based. But the West is on the alert for signs of tension, months after Albanians in neighbouring Kosovo declared independence from Serbia.

Gruevski is expected to pick one of the two main Albanian parties - Ali Ahmeti's Democratic Union for Integration or Menduh Thaci's Democratic Party of Albanians - as a coalition partner to bolster his majority in the 120-seat parliament.