One person was shot dead, nine were wounded and voting was halted in one town after a gun battle. The electoral commission noted instances of suspected fraud and irregularities such as broken or missing ballot boxes and stolen voting materials.
Two of its local officials in the ethnic Albanian Tetovo area were briefly detained by an unknown armed group before being rescued unharmed by police, the commission added.
"I have to express my regret and worry that after the 2006 elections, which were overall evaluated as very good, this year we have bad elections," said commission chief Jovan Josifovski.
The ethnic Albanian Democratic Union for Integration (DUI) leader, former guerrilla commander Ali Ahmeti, blamed the rival Democratic Party of Albanians (DPA) and the police for "provocations, violence and psychological terror".
"What happened today is a black mark on Macedonia," he said.
The two parties are bitter rivals for the vote of the 25 percent Albanian minority. They have been on bad terms since 2006, when the DUI, which won most of the Albanian votes, was left out of a coalition government in favour of the DPA.
The violence is the worst since the end of the 2001 rebellion, when all-out ethnic war was averted by the West using the lure of NATO and the European Union to secure more rights for Albanians and get guerrillas to disarm.
EU foreign policy chief Javier Solana and the United States embassy in Skopje both issued statements expressing concern and calling for restraint. Before the vote, Brussels had said the election is a test Macedonia must pass to start EU negotiations.
The West is worried by any signs of instability in the Balkans so soon after the February secession of Kosovo's ethnic Albanians from Serbia, the latest shudder in a region torn apart by the collapse of Yugoslavia in the 1990s
The situation appeared to have calmed down by the time polls closed at 7 p.m. (1700 GMT). Turnout was around 46 percent by 5 p.m. (1500 GMT)
"The situation in the country overall is stable," Prime Minister Nikola Gruevski told reporters. "The incidents are small in number and mostly in ethnic Albanian areas. There will certainly be a repeat vote in those areas in two weeks."
Gruevski's conservative VMRO-DPMNE party is expected to win the vote on a surge of nationalist defiance after Greece blocked Macedonia's NATO bid in April in a 17-year row over the name it shares with a Greek province.
Gruevski's government, which will likely have to include a partner from the ethnic Albanian parties, will be asked to get NATO accession back on track, start EU membership talks and calm tensions among the rival Albanian factions.
Weeks of minor armed incidents between the Albanian parties during the campaign led authorities and NGOs to engage an estimated 6,000 local and foreign monitors.
The violence on voting day began soon after polls opened.
Scuffles broke out in several Albanian areas and a small explosive device was thrown at an empty cafe. Near Skopje, voting was stopped in the town of Aracinovo after a gun battle.
Police said officers went to the town after local monitors reported the arrival of men with machine guns. They came under fire and retaliated, killing one gunman and injuring two others.
The DUI said the incident was initiated by plain-clothes police.
"They stopped our convoy and shot one round in the air, it was chaos, we got out from the cars and tried to flee," DUI official Shefik Duraku told Reuters.
In Skopje's Cair neighbourhood, another shooting took place outside a polling station. One DUI official was in critical condition and five other people were wounded, police said.
At least 10 people have been arrested in connection with the violence. They included Agim Krasniqi, a commander of the guerrilla Albanian National Army in a 2001 rebellion who remained active after a peace deal was reached.