"An analysis of the number of non-voters as well as blank and disqualified votes reveals a clear anomaly in the final results in Haut-Ogooue" province, Bongo's fiefdom, the observers said in a statement.
Haut-Ogooue is one of the country's nine provinces and turnout there, according to official figures, crossed 99% with 95% voting for the president.
Even after the vote result in the other provinces had been settled, electoral commission members fiercely debated the count for Haut-Ogooue, the heartland of Bongo's Teke ethnic group, before the incumbent was declared the winner on Wednesday.
Thousands of protesters poured onto the streets of the capital Libreville, accusing the governmment of stealing the election.
At least 800 people were arrested in the clashes that followed the news that Bongo had been re-elected.