She had been under house arrest since the 30 August coup.
But after a long hearing in front of a judge it was decided that she should be detained in jail.
Her lawyer, Francois Zimeray, criticised the decision and is quoted as calling it arbitrary and illegal.
Mrs Bongo is facing charges of money laundering, forgery and the falsification of documents. She has not made any public comment on the charges.
The BBC understands she will appear in court in 10 days’ time for a further hearing, where her lawyer can make a case for her release.
The former head of Gabon’s cabinet, Brice Laccruche Alihanga, who was jailed four years ago on charges of embezzlement, misappropriation of public funds and money laundering, gave evidence at Mrs Bongo’s hearing.
The allegations against her are closely linked to the former cabinet chief.
In 2019, the former first lady is alleged to have been behind a major anti-corruption campaign, dubbed Operation Scorpion, which saw several government officials arrested and jailed, including Alihanga, and which some Gabonese described as a witch hunt.
Noureddin Bongo, the son of the deposed president, is also in detention awaiting trial on corruption allegations following his arrest after the coup.
The ousted president, aged 64, had led the oil-rich country since 2009 when he succeeded his father who had been in power for more than 40 years. The family had strong links to France, the former colonial power in Gabon.
The August coup, led by Gen Brice Oligui Ngeuma, was greeted by celebrations at home but has been condemned by regional and continental bodies, as well as France
It came soon after the announcement that Mr Bongo had won disputed elections.
A week after the military takeover, the deposed president was released from house arrest and is free to leave the country, but he has remained in the capital, Libreville.
Gen Nguema has promised that there will be free and fair elections leading to the establishment of a new civilian government, but no timetable has yet been announced.
Source: BBC NEWS
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