The mission said election day was generally calm, but that voting was marred by procedural shortcomings.
EU Enlargement Commissioner Olli Rehn said shortcomings in the preparation and conduct of the elections show the need for better cooperation among political parties.
The vote for local mayors passed peacefully in what was seen as a test of Albania's democratic progress as it bids for EU and NATO membership.
Preliminary unofficial results show the opposition Socialist Party ahead.
(with material from Reuters, AFP)