It comes about after Wilmots told 'beINSports' that he was told that Courtois' father had leaked team selections during the 2016 European Championships.
"Mr Wilmots - not for the first time - reiterates publicly and intentionally (makes) accusations against my honour and my reputation," Courtois said on Instagram.
"As well as my father, we decided together to file a complaint accompanied by criminal indemnification proceedings for libel and defamation."
Courtois has 54 caps for Belgium and barring a major surprise will start for them at the World Cup. Wilmots was dismissed as Belgium manager after they were knocked out of the 2016 tournament by Wales.