His boss, Michel Catalano, had seen the brothers arriving and told him to hide, before letting them in.
Later they let him go.
But local MP Yves Albarello told RMC radio that someone was hiding in the plant and the France 2 and TF1 TV stations later broadcast the information.
Lepère's sister Cindy confirmed in an interview with France 2 that her brother was probably inside and that the family had stopped phoning him to avoid revealing his whereabouts.
Lepère lawyer, Antoine Casubolo-Ferro, welcomed the official investigation, saying that it would "make the media think twice next time".
Another case is already under way against the BFMTV TV channel for revealing that someone was hiding in the cold store of the kosher supermarket in which the Kouachis' accomplice, Amédy Coulibaly, was holed up.
In February the official media watchdog, the CSA, reprimanded seven TV channels and six radios, including RFI and France 24, for their coverage of the Charlie Hebdo attacks, notably for reporting the assault on the Kouachi brothers live.
The broadcasters hit back with the charge that the CSA was inciting self-censorship.
Britain's broadcasting authority did not censure Sky News TV for showing footage of the shooting of police officer Ahmed Merabet outside Charlie Hebdo's offices with the last few seconds when he was shot in the head edited out.
Merabet's brother, Malek, criticised media for showing the footage.