In the latest fallout from last month's launching of the Indonesia Premier League (LPI), the referees were also booted out of the PSSI, the Jakarta Post reported.
The PSSI's director of referees Bambang Irianto said revoking the international licenses of the match officials would leave the LPI struggling for credibility.
"How can they claim that their matches are professional when the (referees) presiding over the matches are referees whose licenses were revoked," he said.
The LPI is an independent professional league launched without recognition from football's governing body FIFA or the PSSI.
The PSSI, which has banned LPI players from playing for Indonesia's national side, has said it had received permission from FIFA to sanction the referees.
Two Singaporean players planning to join LPI side Medan Chiefs have also put their international careers at risk as the Singapore Football Association also refuses to recognise the breakaway league.
