The victims alleged that senior figures in the diocese of Lyon, in eastern France, including Archbishop Philippe Barbarin failed to report the priest, who has been charged with sexually abusing minors between 1986 and 1991, to police.
A formal investigation was opened on January 27 after Bernard Preynat, the priest, admitted he sexually abused young Scouts over 25 years ago.
His lawyer, Federic Doyez, said Preynat told the judge that "the facts had been known by the church authorities since 1991", when he was expelled from the independent Scouts group he had led for nearly 20 years.
In an interview earlier this year, Barbarin, 65, said he had been made aware of the priest's behaviour "around 2007-8" and the Vatican earlier gave the cardinal its backing, saying it had confidence he would deal with the matter "with great responsibility".
Pope Francis, however, has previously said that any bishop who moves priest knowing him to be a paedophile is reckless and should resign.
"This comment does not in any way target Cardinal Barbarin who quite rightly suspended Father Preynat after meeting a first victim and taking advice from Rome, and this, even before a first official complaint was made," a source close to the cardinal said.
The probe comes a day after Vatican finance chief Cardinal George Pell admitted he should have done more to follow-up on claims a priest was abusing boys.
Pell was giving evidence on Thursday to the Royal Commission into Institutional Responses to Child Sexual Abuse in Sydney via videolink from Rome.
Pell has claimed at least two archbishops and other people in authority all deceived him by not revealing what was happening during a period of what he called "crimes and cover-ups".
Earlier on Friday, the Vatican also defended the Church's action on paedophile priests, saying popes Francis and Benedict XVI had "courageously" tackled the issue but admitting there was still much to be done in many countries.
Vatican spokesman Federico Lombardi said "sensationalism" surrounding the Oscar-winning film "Spotlight" and hearings into the alleged cover-up of abuse by Cardinal Pell had given the public the wrong impression.
The media furore surrounding both events "meant that most people, particularly those less well informed or with a short memory, think the Church has done nothing or very little to answer to these horrible tragedies", he said.
"An objective consideration shows it is not true," he added in a statement.
Some abuse victims insist the Vatican still has not gone far enough to protect children even in the West -- where intense media coverage of paedophile priests has led to greater scrutiny of church practices.
"Spotlight," which chronicles The Boston Globe's investigation into sexual abuse in the Catholic Church and institutional efforts to cover up the crimes, won the Oscar for best picture last month.