One man told the AFP news agency the "French ... come here to eat
"All the presidents who have come to this palace have left again with their pockets full and then you criticise us."
Security guards quickly formed a cordon around the French leader as he went into the presidential palace.
Bernard Kouchner, the French foreign minister, and Jacques Chirac, France's former president, were also present as part of the French delegation to the funeral, a reflection of the modern day role France sees itself as playing in its former colonies.
The state funeral began inside the marble halls of the palace, a towering edifice Bongo reportedly spent about $800m to build.
The red carpet leading to his coffin was strewn with white rose petals flown in from France.
Outside the palace, mourners thronged the streets of the capital.
Thousands of people had lined up over the course of five days to pay their respects with some sleeping outside the gates of the presidential palace.
Ali Ben Bongo, Gabon's defence minister and the late president's son, who is widely tipped as likely to take over leadership of the country, spoke for the family at the funeral service.
"We, your children, your family, make a solemn commitment to keep alight with the aide of our fellow citizens the sacred flame of family harmony, republican concord and national unity," he said.
After a minute's silence, guests took turns to kneel briefly in front of Bongo's coffin draped with the national flag, before it was taken out for a two-hour military parade on the Atlantic seafront.
African heads of states also paid their respects, with Paul Biya, Cameroon's president, and Blaise Compaore, the president of Burkina Faso, laying wreaths at the foot of the coffin.
By the time he died in a clinic in Spain, where he was reportedly receiving treatment for cancer, Bongo had been in power longer than any other leader in Africa.
Rose Francine Rogombe, the speaker of Gabon's senate, is the country's interim-president ahead of elections.
Sarkozy denied there would be any French interference in the selection of a successor.
"France has no candidate ... it is not supporting anyone," he said on the sidelines of the service.
Relations between Gabon and its former colonial master cooled when, two years ago, a French court launched an investigation into the late leader's massive property holdings in France, which include at least 37 apartments in Paris alone.