The news came on an already tumultuous day for Brisbane which signalled the resignation of club stalwart Andrew Gee, ending a 25-year association with the club.
The NRL have begun an investigation after Brisbane last week alerted league bosses to a number of serious cap-related issues involving the club's recent recruitment activities, News Corp says.
"The Brisbane Broncos have advised the NRL of some possible salary cap irregularities and asked us to look at them which we will do," an NRL spokesman told The Courier-Mail website.
The probe will reportedly examine third-party agreements and the fact at least one-big name player is owed a six-figure sum.
News Corp says the player in question is allegedly owed money by the Broncos in relation to third-party sponsorships.
There is no suggestion Gee is guilty of orchestrating a cap breach.
Ex-Test and Queensland Origin prop Gee walked away from his role as general manager of football operations role on Tuesday.
It came after he took leave from the club a fortnight ago to consider his future.
Broncos under-20s team manager Scot Czislowski will take over team manager roles for the club's NRL squad from Gee, who played 255 games and won three flags with Brisbane.
Peter Nolan will continue to work in the list and recruitment manager's position he was recently appointed to.
"The Broncos acknowledge the significant contribution Andrew Gee has made in his current role and in his former roles as both a player and an administrator over a 25-year period," the Broncos said in a statement.
"The club wishes both him and his family all the best for the future."
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