Fourteen soldiers have been placed under investigation, following statements by six children aged between nine and 13 that some were sexually abused by French peacekeepers between December 2013 and June 2014.
The announcement came a day after the Central African Republic government said it would launch its own legal action against the French soldiers.
"We regret the fact we were not brought into these investigations despite the cooperation agreements we have with France," said Justice Minister Aristide Sokambi.
French troops were deployed to the Central African Republic in December 2013 to help African Union peacekeepers restore order after a bout of sectarian bloodletting triggered by a coup.
Hundreds of troops were stationed outside the capital Bangui at M'Poko airport, which was transformed into a giant refugee camp.
Most of the displaced families living amid the abandoned planes had lost everything in the conflict, which pitted mainly Muslim rebels against vigilantes from the majority Christian population.
The defence ministry has said it immediately launched a probe into the rape allegations when they were first received in July, sending police investigators to the former French colony on August 1st.
But the damning allegations only became public after The Guardian newspaper broke the story last month.
The allegations were first collated in an internal United Nations report and only reached French authorities when it was leaked by a senior UN official.
Both the French government and UN have denied trying to cover up the potentially devastating scandal, but the UN official was suspended from his job over the leak.
If proven, the allegations will not only affect the French army but also the Central African Republic, which is trying to find a way out of a conflict that has killed thousands and displaced nearly 900,000 people.