Cardinal Philippe Barbarin hit back, insisting at a press conference: "I have never covered up paedophilia."
The latest abuse scandal to hit the Catholic Church erupted when priest Bernard Preynat was charged in January, after victims came forward with claims he had sexually abused Scouts between 1986 and 1991.
Prosecutors say he has admitted the charges.
The victims have filed complaints against several senior officials in the Lyon diocese in eastern France, including Lyon archbishop Barbarin, accusing them of being aware of the abuse but failing to report the priest.
Barbarin has argued he was not archbishop at the time when the first complaints emerged against Preynat - who was briefly suspended and then moved to another parish.
Accusations were made against Preynat only when a victim who was allegedly abused in the 1980s realised in 2015 that the priest was still in service. Other victims have since come forward.
The case recalls the recent Oscar-winning film "Spotlight", which highlighted how the Church transferred deviant priests between parishes in Boston in the US.
Barbarin has said he learned of Preynat's "behaviours" in 2007 or 2008, and met with him "to ask if, since 1991, anything had happened; he assured me there had been absolutely nothing.
"Some blame me for believing him... Yes, I believed him," Barbarin said in an interview with Catholic newspaper La Croix.
The diocese removed Preynat from service in May 2015.
The Vatican has backed the cardinal, saying he had shown "a great deal of responsibility" in dealing with the matter.
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