The case could strain French diplomatic and business ties with Gabon and Congo Republic, two former colonies and close allies, and with Equatorial Guinea, a growing oil exporter.
"This is an unprecedented decision because it’s the first time a judicial inquiry has been opened concerning suspected embezzlement by sitting presidents," said William Bourdon, a lawyer representing the plaintiffs in the case.
A 2007 French police probe found the leaders of the three countries and their families owned dozens of bank accounts, homes in rich areas of Paris and on the Riviera, and cars including Bugattis, Ferraris, Maybachs, Maseratis and a Rolls-Royce.
Omar Bongo of Gabon, Denis Sassou-Nguesso of Congo and Teodoro Obiang Nguema Mbasogo of Equatorial Guinea deny any wrongdoing. They have been embarrassed by the disclosure in French media of their assets worth tens of millions of euros.
Bongo, Africa’s longest-serving ruler who regards Paris as a second home, was so infuriated by a report on the subject on French state television last year that the French ambassador in Libreville was summoned in protest.
The Paris magistrate, who is independent from government, decided to open the formal investigation at the request of the French arm of anti-graft watchdog, Transparency International.
It is the first time the organisation has been admitted as a plaintiff in such a case and the precedent is likely to encourage similar actions by anti-graft activists elsewhere.
A Gabonese citizen, Gregory Ngbwa Mintsa, had requested to be a co-plaintiff with Transparency on the basis that as a taxpayer he was a victim of corruption, but the magistrate rejected the argument so he will not be party to the case.
The Paris prosecutors’ office, which answers to the justice ministry, had asked for Transparency’s complaint to be shelved. It is likely to appeal against the magistrate’s decision.
Should the case continue, it could damage France’s relations with two of its closest African allies, but if it is halted that would raise suspicions some presidents are protected because of French interests in their countries.
Bongo and Sassou-Nguesso have both enjoyed friendships with successive French presidents and backing from Paris at testing moments of their careers.
French oil and gas group Total is the leading producer in Gabon and Congo Republic and many other French firms, public and private, have long-term contracts there.
The magistrate has opened a preliminary investigation, which in French law is a first step towards establishing whether there may be a case to answer in a criminal court.
It can lead either to further investigation or to no further action.