Ministers said the Scottish Catholic Education Service would continue to decide on the faith content of the curriculum in Catholic denominationalschools.
The Post Primary Transfer Consortium (PPTC) provides the GL assessment tests mainly for Catholic grammars, along with some integrated colleges and a few non-denominational schools.
This included changing its policy on providing free transport to denominationalschools, which had been granted irrespective of whether pupils could provide evidence of their faith.
Prosecutors have asked for reports to be prepared as they consider an appeal against the ruling in Mr McLeish's case, in which the sheriff stated sectarianism should be tackled by abolishing denominationalschools.
Many liberal Jews still see sectarian day schools as somehow un-American, and the relatively few Conservative and non-denominational day schools have seen a drop in enrolment since the 2008 financial crisis.