Cardinal Godfried Danneels, who stepped down in January after three decades as Belgium's archbishop, has been accused of knowing of sexual abuse but failing to stop it.
"He was named in at least 50 files as being aware (of the abuse cases)," a spokesman for the Belgian prosecutor's office said.
Danneels has not responded in public to the accusations and has not been charged with any crime.
Bishops conference spokesman Eric De Beukelaer has said the Belgian Catholic Church is ready to cooperate with the investigation.
A separate examination has also been launched into the inquiry itself to ensure the rules are followed properly.
"This affair is so important that you have to check from the start the procedures are being followed correctly," said the spokesman for the prosecutor's office.
A church commission monitoring complaints about sexual abuse of children by priests was disbanded last week after police seized all of its 475 files and the computer of its chairman, Peter Andriaenssens.
The documents were seized during coordinated raids in which police drilled into two tombs in the crypt of Mechelen Cathedral in northern Belgium and inserted tiny cameras to find out if any files had been hidden there.
The raids were a further embarrassment for the Belgian Catholic Church following the resignation of Bruges Bishop Roger Vangheluwe in April after he admitted sexually abusing a boy many years earlier.
His admission prompted a wave of abuse complaints to the commission. Child abuse is a particularly sensitive issue in Belgium, where perceived police incompetence over paedophile killer Marc Dutroux provoked mass protests in the 1990s.
SIC: ReutersUK