One of the most contentious issues is how to ensure the fair representation of women - with questions arising over how to implement a legally required quota system setting aside seats for them on the councils.
The confusion stems from the election law that sets guidelines for the vote. The measure was enacted in November after months of bitter debate among rival ethnic and religious factions.
Members of the Independent High Electoral Commission, which oversees balloting, said the law was unclear on certain points, including how to allocate seats based on the number of votes received.
Lack of clarity has forced the commission to make its own interpretations in establishing the specific guidelines for the vote.
Commission chief Faraj al-Haidari singled out the women's quota system, saying the committee had decided to mandate one female winner for every two men because the law did not take into account smaller parties without female candidates.
"The elections law says that for every four winners there is a woman, but the commission had another interpretation," he said. "This is not applicable in the small entities that have only one or two people, and this might mean that women might get less than their stated quota."
Jalaluddin al-Saghir, a lawmaker with the biggest Shiite party, said the issue could prove problematic.
"I think this process will create problems in the end because some male candidates will feel that some women have won despite the fact that they had fewer votes," he said.
The electoral commission also said it had taken measures to minimize confusion at the polls since voters for the first time will be allowed to choose candidates instead of just political parties.
But the voters must understand that a vote for a political party is required while individual candidates are optional.
Candidates' names won't appear on the ballot. Instead they will be identified by numbers posted in the polling station.
Officials decided not to include names of candidates on the ballots because of the large number - 14,431 nationwide, competing for 444 council seats.
