Although the church repeatedly lost in legal cases which were heard up to the level of the Supreme Court, it undertook negotiations with the IRS from 1991 to find a settlement. In October 1993, the church and the IRS reached an agreement under which the church discontinued all of its litigation against the IRS and paid $12.5 million to settle a tax debt said to be around a billion dollars, and the IRS granted 153 Scientology-related corporate entities tax exemption and the right to declare their own subordinate organizations tax-exempt in future.
The terms and circumstances of the agreement remained secret until details emerged through leaks and litigation from 1997 onwards. They have attracted controversy for their perceived favorability towards the church and have been described as unconstitutional by federal courts for their bestowal of privileges on Scientologists that are shared by no other religious group. Questions have also been raised about whether the IRS exceeded its authority by effectively overruling the Supreme Court in setting the terms of the agreement and permitting tax deductions not authorized in law. However, legal commentators have concluded that the agreement can effectively no longer be challenged in court.