The commission reviewed 56 complaints from political parties that cited irregularities involving about 300 polling stations out of a total of 2,976.
Political parties and coalitions can appeal the commission's ruling to the Supreme Court within 48 hours of its announcement. The court must rule on the appeal within another 48 hours.
If the high court upholds the commission ruling, another round of voting will be conducted June 15 at all 186 polling stations.
Gunbattles and reports of ballot fraud in ethnic Albanian areas prompted authorities to suspend voting in 22 polling stations on Sunday. One person was killed and eight were wounded in the fighting, which brought international condemnation at a time when Macedonia is trying to prove its credentials for European Union and NATO membership.
About 50 people have been detained over the last three days in connection with the violence and irregularities. A court ordered at least 30 of them to be held for 30 days - including one policeman.
Next weekend's reruns could determine which of the two main - and bitterly opposed - ethnic Albanian parties will be invited into a governing coalition: DUI, run by former rebel leader Ali Ahmeti, or the Democratic Party of Albanians, run by Menduh Thaci.
Although Prime Minister Nikola Gruevski, 37, won by a landslide 48.2 percent, enough to give him a majority in the 120 seat parliament, it is traditional to invite one of the Albanian minority's parties to join the government.
Ethnic Albanians make up about a quarter of Macedonia's population. A six-month ethnic Albanian insurgency in 2001 ended after a Western-brokered peace plan.
According to initial results, the DPA, which is part of the outgoing governing coalition, won 10.52 percent, or 105,000 votes, compared with DUI's 11.13 percent, or 111,000 votes.
Based on the figures, each party projects it would win 13 seats in the 120-seat parliament. The much smaller Party for Democratic Prosperity, the oldest ethnic Albanian party, appears to have won one seat in parliament and has announced it will join DPA, giving Thaci a slight edge.