In Tuesday's divided U.S. Supreme Court decision on state funding of religious schools, a dissenting Justice Stephen Breyer issued a warning to his conservative colleagues that they were encouraging the very religious conflicts that the Constitution's drafters sought to avoid.

"The majority's approach and its conclusion in this case, I fear, risk the kind of entanglement and conflict that the religion clauses are intended to prevent," Breyer wrote.

Chief Justice John Roberts Jr. led the 5-4 conservative majority in the ruling in Espinoza v. Montana Department of Revenue, which said taxpayer-funded scholarships must fund private religious schools if they also fund private secular schools. To do otherwise, he concluded, violates the First Amendment's free exercise clause.

"A state need not subsidize private education," Roberts wrote. "But once a state decides to do so, it cannot disqualify some private schools solely because they are religious."

But Breyer warned that hard feelings, for example, among taxpayers who don't want to finance the teaching of religious beliefs or among religious minorities too few in number to support a school of their own, may "in turn, sow religiously inspired political conflict and division." That risk, he added, "is considerably greater where states are required to include religious schools in programs like the one before us here. And it is greater still where, as here, those programs benefit only a handful of a state's many religious denominations."

The court's decision comes at a time of increasing controversy over the Trump administration's efforts to push greater government accommodation and protection of religious organizations. The administration's Education Department has made school vouchers for religious schools a priority. The Health and Human Services Department has expanded religious and moral exemptions to contraceptive health insurance requirements in the Affordable Care Act. And the Justice Department has intervened to argue against state restrictions imposed in the coronavirus era on religious gatherings.

In a speech in October, U.S. Attorney General William Barr said religion has been under attack for the past 50 years and religious liberty is a department priority. "On the one hand, we have seen the steady erosion of our traditional Judeo-Christian moral system and a comprehensive effort to drive it from the public square," he told an audience at Notre Dame Law School. "On the other hand, we see the growing ascendancy of secularism and the doctrine of moral relativism."

Chief Justice John Roberts Jr. appearing last week at Belmont University in Nashville. Screen grab via YouTube.

During the past two weeks, Roberts has surprised both ends of the political spectrum with either leading or joining rulings sought by progressive groups. But there was little surprise about his position in the Espinoza case. He and his conservative colleagues have favored religion clause claims, particularly free exercise ones, in recent decisions and statements, following the trend in the prior Rehnquist and Burger courts.

The Montana case was the third religion-related case on the term's argument docket. Decisions in the remaining two have yet to be issued: Trump v. Pennsylvania, involving federal religious and moral exemptions from the contraceptive insurance requirement in the Affordable Care Act, and Our Lady of Guadalupe School v. Morrissey-Berru, concerning the so-called ministerial exception to federal anti-discrimination law.

Roberts based his decision in the Montana case primarily on his ruling in 2017 in Trinity Lutheran Church v. Comer. That decision held that excluding a church from a state-funded playground resurfacing program violated the First Amendment's free exercise clause. The discrimination in the Montana case, as in Trinity Lutheran, he wrote, was because of religious status.

But Breyer countered, "As I see the matter, our differences run deeper than a simple disagreement about the application of prior case law."

The Montana case stemmed from a lawsuit from three parents who challenged a ruling by the Montana Supreme Court. The state court had invalidated a state tax-credit program that generated school scholarships. The challengers said they were counting on the scholarship money to keep their children in a religious school.

The program provided a dollar-for-dollar tax credit of up to $150 for individuals and businesses who donated to private scholarship organizations, which then used the funds for scholarships to students who wanted to attend private schools. In Montana, private schools are overwhelmingly religious.

Soon after the program's creation by the legislature, the Montana Department of Revenue issued a rule that families could not use the scholarships at religious schools because Article X of the state constitution barred aid for churches and religious schools. Jenner & Block's Adam Unikowsky argued at the high court for Montana.

The parents argued that the department's interpretation and application of Article X violated the federal Constitution's free exercise, equal protection and establishment clauses. They also contended that Article X is a so-called "Blaine Amendment," with origins in anti-Catholic bigotry.

Besides Breyer's disagreement with Roberts on whether Trinity Lutheran applied to the Montana situation, his dissent also focused on his differences with Roberts on the history of the establishment and free exercise clauses and the Founders' efforts to maintain separation of church and state. But he devoted a substantial part of the dissent at the end to his view of the decision's consequences.

Breyer posed, among other questions: "What about a religion that objects to the particular way in which the government seeks to enforce mandatory (say, qualification-related) provisions of a particular benefit program? Or the religious group that for religious reasons cannot accept government support? And what happens when qualification requirements mean that government money flows to one religion rather than another? What about charter schools?"

Courts, he wrote, are ill-equipped to deal with the types of conflicts that may arise. "Yet, in a nation with scores of different religions, many such disagreements are possible. And I have only scratched the surface."

Justice Ruth Bader Ginsburg, joined by Justice Elena Kagan, wrote a separate dissent. Kagan also joined Breyer's dissent. Justice Sonia Sotomayor also dissented in a separate opinion.