The man in charge of assigning Serie A and B referees, Gianluca Rocchi, has suspended himself from the role with immediate effect while under investigation for sports fraud by Milan's Public Prosecutor's Office.
VAR supervisor Andrea Gervasoni has taken similar action for the same reasons, and the investigation is looking into incidents during last season's Serie A campaign.
"This choice, painful, difficult but shared with my family, is intended to allow the legal proceedings to run their course properly, from which I am sure I will come out unscathed and stronger than before," Rocchi's statement to Italy's referees' association (AIA) said.
According to Italian media reports, Rocchi is accused of interfering with VAR protocols along with selecting referees preferable to Inter Milan.
"We are learning everything from the media, so we are stunned by the declarations," Inter President Giuseppe Marotta told Sky Sports before his side's game at Torino on Sunday.
"We do not have referees that we favour or are unfavourable towards, we are confident that we acted entirely fairly, which should reassure everyone.
"We are safe in the knowledge that Inter are not involved in this situation and will not be involved in the future."
The news has sparked fears in Italy of another crisis, similar to the Calciopoli match-fixing scandal which saw Juventus stripped of the 2004-05 Serie A title and relegated to Serie B, with AC Milan, Fiorentina, Lazio and Reggina also involved.
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