With a population that is more than 60 percent illiterate, polling station staff marked ballots for many people, the election monitor said.
The election monitor does not plan to count 34,331 challenged ballots.
However, election monitors observed a "small number of serious irregularities," particularly during vote counting.
However international election monitors reported that they did not find any irregularities in the election.
Despite this, international election monitors declared the polls valid and said the results should not be invalidated.
The election was the first in Jamaica where a team of international election monitors attended.
That made it all the easier for the people to trust the Federation as impartial election monitors.
Local, statewide and national assembly elections since December were judged generally fair by election monitors.
The approval of international election monitors is important not only for Nigeria's international image.
The election monitor said that the local has 52,000 members, down sharply from the 70,000 the union claimed three years ago.