Bongo's eldest son Noureddin Bongo Valentin and former presidential spokesman Jessye Ella Ekogha "have been charged and placed in provisional detention" on Tuesday over alleged corruption, said Libreville prosecutor Andre-Patrick Roponat.
In all, 10 people were indicted on Tuesday with charges ranging from electoral college operational issues, counterfeiting and use of the seals of the republic, to corruption, embezzlement of public funds and money laundering, Roponat told a press conference.
Bongo, 64, who had ruled the oil-rich central African country since 2009, was overthrown by military leaders on Aug. 30, moments after being proclaimed the winner in a presidential election.
The result was branded a fraud by the opposition and the military coup leaders, who have also accused his regime of widespread corruption and bad governance.
On the same day as the coup, soldiers arrested one of Bongo's sons and five senior cabinet officials.
National TV showed rolling images of those arrested in front of suitcases filled with cash allegedly seized from their homes.
Bongo's wife Sylvia Bongo Valentin is under house arrest in the capital Libreville "for her protection," according to authorities. Her lawyers say she is being held "arbitrarily."
Bongo, who was himself under house arrest for several days after the coup, is "free to move around" and go abroad, Gabon's new military ruler Gen. Brice Oligui Nguema said on Sept. 6.
Oligui has been sworn in as interim president after spearheading the coup that ended a half-century of rule by the Bongo family.
He has promised to hold "free, transparent and credible elections" to restore civilian rule but has not given a timeframe.
Shortly after the coup, the new strongman warned business chiefs that corruption would no longer be tolerated.
Ali Bongo took over when his father Omar died in 2009 after nearly 42 years in power.
In 2016, French investigators zeroed in on properties owned by Omar Bongo's family in France.
They suspected several of his relatives had knowingly benefitted from a fraudulently acquired real-estate empire worth at least 85 million euros ($87 million).
Ten of Omar Bongo's 54 children have been charged with allegedly concealing the misappropriation of public funds, a Paris-based legal source has told AFP.
As a sitting head of state, Ali Bongo had immunity.
Editor's Note: This article was corrected to remove charge of high treason after contradictory statement by the prosecution.