Required chapel attendance, required courses in religion and the Bible, student admissions or faculty hiring based on religious identity could be targeted by lawsuits under the proposed law, he said.
The legislation would "carve away at the ability of these universities and colleges to operate in a manner that is consistent with their faith values."
If the schools will not change their beliefs, they will have to refuse to take CalGrants. The grants allow disadvantaged students to access higher education at a college or university of their choice, including schools consistent with their religious beliefs.
About 25 percent students at religious schools are CalGrant recipients. Among these students, about 80 percent come from disadvantaged populations. At some schools, as many as 40-45 percent of the student body is on CalGrants.
Some schools might not be financially sustainable without taking CalGrant students.
"My hunch is that we would probably see a few schools that would have to close in the state of California," Mannoia said. "Certainly all the faith-based institutions would have to realign their priorities in an effort to replace that money."
He said that even if the funds were replaced through other means, the more serious issue in the long term is the religious freedom of those institutions to govern and hire in a way consistent with their faith.
This ability "is in jeopardy and becomes exposed to public liability."
Mannoia said that supporters of the colleges and university should contact the California legislature to object to the bill.
"This is not a time for the Church to become vitriolic or antagonistic. It is not a time to bash any group in our culture at all in an attempt to defeat it," he said.
"This is a time for Christian higher education, for faith-based institutions, to tell their stories. This is a time for us to frame this around the big issues of religious freedom, choice of students and access of students to higher education."
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Kevin J. Jones is a senior staff writer with Catholic News Agency. He was a recipient of a 2014 Catholic Relief Services' Egan Journalism Fellowship.