The country's electoral commission also said there were instances of suspected fraud and irregularities such as broken or missing ballot boxes and stolen voting materials.
Erwan Fouere, head of the European Union office in Macedonia, said he was "deeply concerned" by the situation.
"We are entering now the critical hour ... before the polls close, and we have appealed to the government and the state authorities to do everything possible to prevent further violence," he said.
Voting was suspended about one per cent of all polling stations in the country due to irregularities and intimidation, Zoran Tanevski, an elections commission spokesman, said.
About 13,000 police were deployed at polling stations after two ethnic Albanian parties blamed each other for violence during the campaign.
|Voting got under way in Skpoje, the|
Macedonian capital, on Sunday [AFP]
Voting was suspended in Gurgurnica near Tetovo in the country's ethnic Albanian northwest after men armed with machine guns appeared at a polling station, Tanevski said.
but the violence was reportedly concentrated in ethnic Albanian areas in Macedonia's northwest.
Ethnic Albanians make up a quarter of Macedonia's 2.1 million people.
The Democratic Union for Integration (DUI), the largest ethnic Albanian opposition party, said its party's headquarters in Skopje, the capital, had come under fire.
There were also reports of ballot-stuffing and allegations of fraud in villages around Skopje during the early hours of voting.
The centre-right VMRO-DPMNE party of Nikola Gruevski, the prime minister, has a sizeable lead and is expected to win, according to opinion polls.
One poll gave him 31.3 per cent of the votes compared to 11.2 per cent for his nearest rival, the Social Democrats.
Before voting got under way international monitors recorded 13 reports of attacks against the DUI, including an incident in which attackers shot at the car of Ali Ahmeti, the party leader.
"DUI was the target of provocation, of violence, of attacks, but we have never sought to retaliate because we refuse to submit to [violence]", Xhevat Ademi, a high-ranking party official, said.
Ademi said the rival Democratic Party of Albanians (DPA) was "nervous" because "DUI will win the elections". Ethnic Albanians make up about 25 per cent of Macedonia's population.
Imer Selmani, the outgoing health minister and vice-president of the DPA, said the DUI was frustrated at having been out of power for almost two years.
"Our political adversaries are presenting themselves as victims when in fact they never stop raising the threat of a return to 2001," he said, in reference to the year the minority fought a six-month insurgency against state forces which was ended by a western-brokered peace deal.
The DPA withdrew its support for his government in mid-March, in protest at its failure to recognise the independence of Kosovo, which stalled the government's efforts to continue with integration into the European Union.
If Gruevski fails to win a landlside he is likely to need the support of the DPA or the DUI to form a government.