The court, which deals with cases against top officials,said in a statement Friday that it threw out 44 of the 90 complaints, and is still studying 37 of them.
They are accused of “failing to fight a disaster," and could face up to two years in prison and fines, if tried and convicted.
That was the only charge the court retained among multiple accusations in the 90 complaints, which included allegations of manslaughter and endangering lives. A conviction on those charges carries the potential for heavier prison terms.
Ten of the cases were closed because they didn’t provide enough justification for an investigation, according to a judicial official. The court said another 34 cases, targeting different government ministers, were thrown out for technical problems.
Macron himself cannot be targeted by lawsuits while in office because sitting presidents have immunity from prosecution.
On Friday, the French leader named as the new prime minister a longtime civil servant who coordinated France's strategy to reopen and recover economically from a two-month nationwide lockdown.
No mention was made of the investigation or legal troubles when Philippe resigned earlier in the day. Macron said he was reshuffling the government to focus on setting a “new path” for the remaining two years of his presidential term.
The Court of Justice of the Republic is the only French court where government ministers can be tried for their actions while in office, and was created in the wake of a major health scandal in the 1990s.
The new investigation is separate from dozens of lawsuits filed in other French courts against nursing homes or others accused of mismanaging the virus crisis.
France has reported the fifth-highest number of coronavirus deaths worldwide, for a total of 29,893 in the pandemic. About half took place in nursing homes.