The Supreme Court, in a 5-to-4 decision, handed a victory to religious educational organizations Monday. (Evan Vucci/AP)

The Supreme Court on Monday made it harder for taxpayers to bring court challenges of government programs that aid religious organizations, throwing out a lawsuit against an Arizona tax-credit program that helps private schools.

The 5 to 4 decision split the court along ideological lines, and prompted the first written dissent by Justice Elena Kagan. She criticized the court’s majority and the Obama administration, in which she previously served, for its arguments on Arizona’s behalf.

The ruling, she wrote, “threatens to eliminate all occasions for a taxpayer to contest the government’s monetary support of religion.”

In general, individual taxpayers do not have the legal right, or “standing,” to challenge spending decisions of government. But the Supreme Court in the 1968 decision Flast v. Cohen agreed to a narrow exception when the spending is alleged to violate the Constitution’s prohibition on establishing religion.

Monday’s ruling, written by Justice Anthony M. Kennedy, emphasized how narrow the exemption was. And he said the court should be careful about getting involved in disputes between taxpayers and their representatives.

Otherwise, he said, the court could become “a Council of Revision, conferring on itself the power to invalidate laws at the behest of anyone who disagrees with them.”

For 13 years, Arizona has allowed a resident to send up to $500 of the money he owes the state in income taxes — $1,000 for a married couple — to a private “student tuition organization.” In other words, if a couple owed the state $2,000, they could send half the money to the state treasury and half to one of the tuition organizations.

The organizations, which receive about $55 million a year, provide scholarships to private schools, often religious ones. The largest of the organizations benefits Catholic schools in the Phoenix area.

Challengers said the program was unconstitutional because it transferred funds that otherwise would have gone to the state treasury. The U.S. Court of Appeals for the 9th Circuit said their suit could go forward.

But Kennedy made a distinction between a government expenditure and a tax credit.

“When Arizona taxpayers choose to contribute to STOs they spend their own money, not money the state has collected from respondents or from other taxpayers,” Kennedy wrote. He added that “objecting taxpayers know that their fellow citizens, not the state, decide to contribute and in fact make the contribution.”

The decision did not directly hold the program constitutional, but said those objecting had no standing to challenge it.

He was joined by Chief Justice John G. Roberts Jr. and Justices Antonin Scalia, Clarence Thomas and Samuel A. Alito Jr. Scalia and Thomas also wrote separately to say they would eliminate the Flast exception.

Kagan said that distinction between spending and tax credit “has as little basis in principle as it has in our precedent.”

She said the opinion “offers a roadmap — more truly, just a one-step instruction — to any government that wishes to insulate its financing of religious activity from legal challenge.”

She wondered why the same concept could not be applied to states that wanted to reward Jews for their devotion or be used by a state to subsidize crucifix ownership.

One option would be to purchase crucifixes and distribute them, or it could reimburse an individual who buys one, she said.

“Or it could authorize that person to claim a tax credit equal to the price she paid,” Kagan wrote. “Now, really — do taxpayers have less reason to complain if the state selects the last of these three options?”

She was joined by Justices Ruth Bader Ginsburg, Stephen G. Breyer and Sonia Sotomayor.

The Supreme Court in 2002 approved the use of taxpayer money on private school vouchers, which could be used at religious schools. And Monday’s decision was the second in which the Roberts court limited access to the courts for taxpayers challenging government spending on religious organizations.

The Institute for Justice, one of two conservative legal groups arguing that those challenging the Arizona program lacked standing, called the decision a major victory for school choice.

American Civil Liberties Union legal director Steven R. Shapiro said the “disappointing” decision in Arizona Christian School Tuition Organization v. Wynn “ignores precedent, defies logic and undermines the role of the courts in preserving the core constitutional principle that government may not subsidize religion.”

In other action Monday, the court agreed to hear the case of a New Jersey man who was stripsearched after being stopped for a traffic violation. As security precautions have increased, courts around the country have differed on when authorities may impose such searches on those accused of minor offenses.

The case is Florence v. Board of Chosen Freeholders.

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