IRS officials say the groups failed to file annual reports over the past three-years.
Jesse Weller is with the Internal Revenue Service's Northern California office in Oakland.
"Most of the organizations, we believe are defunct and no longer in existence because the IRS has made a substantial effort over the last three to four years trying to notify these organizations of the new filing requirements."
Weller says still-functioning organizations that didn't get the message can reapply for reinstatement of their tax-exempt status.
A 2006 law requires most tax-exempt organizations to file an annual information return with the IRS.
It automatically revokes the status for groups that fail to file the required papers for three consecutive years.