Newly tattooed Messi wearing Bermuda Shorts and a T-shirt was on an official visit to lay the foundation stones for a new stadium.
But the Barcelona and Argentina caused outrage when he helped open a new Bongo family restaurant showing support for their regime.
"People are outraged about this," said an opposition source in the country.
The country is notoriously known for corruption and linked to human rights abuses.
According to French media Messi and his former Barcelona team-mate Deco were paid £2.4 million for the trip.
One photograph shows the player placing his hands in cement at the stadium in Port-Gentil.
"The little African trip should bring in around 3.5 million euros. Not bad!" read a report in France Football.
But Bongo fiercely defended Messi's appearance and said "When I was in Barcelona a few years ago, I met Messi who had told me that he would come to visit me in Libreville.
"It's a promise he made me. He is a man of honour who just kept his word."
French cops routinely investigate corrupt allegations against the Bongo family – who are alleged to own 39 homes across the country including Paris.
The CIA/World Factbook reads that Gabon's per capita income is four times that of most sub-Saharan African nations.
The World Bank said almost one-third of Gabonese live at or below the poverty line.
Messi himself is not clean cut - he is facing trial for tax fraud in Spain.
Barcelona High Court believes he has made money from a complex network of companies which hid £3m pounds from Spanish tax authorities between 2007 and 2009.
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