The inquiry will be led by the Law Court of the Republic (CJR), which deals with claims of ministerial misconduct, said senior prosecutor Francois Molins.
Along with Philippe, who was replaced Friday in the first stage of a government reshuffle, the ministers under investigation are former health minister Agnes Buzyn — who stepped down in February for an unsuccessful bid to become mayor of Paris — and her successor Olivier Veran. Veran was health minister during the peak of the crisis.
It is not clear if he will keep his job in the reshuffle expected to be finalised in the coming days.
The CJR has received 90 complaints and examined 53 of them.
It considered nine complaints admissible, which will form the basis of the inquiry. The complaints were filed by private individuals, doctors, associations and even prisoners. The inquiry will consider whether Philippe, Buzyn and Veran neglected their duties in the face of a disaster.
The coronavirus outbreak has left 29,875 people dead in France so far, and has sparked anger against the government over a lack of protective equipment in the early stages of the pandemic.
France is not the only country where legal proceedings are possible against current and former ministers over the coronavirus pandemic.
Prosecutors questioned the Italian prime minister and two ministers last month over their handling of the coronavirus crisis as part of an investigation into whether more should have been done to save lives.