The runoff is being held in 57 of Macedonia's 84 municipalities, among others in the capital of Skopje.
The opposition, united around independent mayoral candidate Trifun Kostovski, claims the ruling coalition falsified the election results for the capital's mayor two weeks ago.
There were problems with the election results in the first round also in western Macedonia, in Albanian majority areas, prompting the opposition Democratic Party of Albanians to call on supporters to boycott the runoff due to "obvious irregularities".
The first round was monitored by some 400 foreign observers, who complained about numerous suspicious events which marred the voting.
Western diplomats have cautioned Macedonia that the municipal elections are a crucial test of the country's ability to adopt Western standards and an important element in its integration into the European Union.