The Supreme Court on Monday ruled in favor of deferring to administrative agencies in determining the scope of their own jurisdiction, issuing a 6-3 decision that featured a sharp dissent from Chief Justice John Roberts Jr.

The decision was one of four issued Monday—none of them the marquee cases the Court is expected to rule on before the end of June. Late May is when the court clears the underbrush of somewhat easier and less hot-button cases in advance of the blockbusters that dominate June. The court has handed down 46 decisions so far this term, with 30 left to go. The court also granted review in five new cases to be decided next term, including a potentially major First Amendment Establishment Clause dispute.

Scalia’s majority opinion in City of Arlington, Texas v. FCC amounted to a strong embrace of so-called "Chevron deference" to administrative agencies, which had eroded somewhat in recent years. Chevron v. Natural Resources Defense Council is the 1984 ruling that gave administrative bodies substantial deference in interpreting ambiguities in laws they administer.

In the case before the court, Arlington and San Antonio, Texas questioned whether the FCC had jurisdiction to enforce a rule it promulgated in 2009 to speed up the local approval process for siting cellular phone towers. The U.S. Court of Appeals for the 5th Circuit sided with the FCC, finding that under Chevron, the FCC deserved deference on the threshold question of jurisdiction as well as the interpretation of governing statutes. Scalia’s majority upheld the 5th Circuit and the FCC’s jurisdiction.

The case drew wide but divided interest from the telecom industry, which wanted the court to endorse FCC jurisdiction over facilitating cellular service – but not in other areas where they would like to see less FCC regulation. Some business groups were disappointed in the ruling, seeing it as an opening for administrative agencies to grab even broader power over the economy and individuals.

"Recent events have proven that federal agencies can’t regulate themselves," said Karen Harned of the National Federation of Independent Business in a statement. "Our government’s foundation relies on the checks and balances between the three branches of government: legislative, judicial, and executive …This ruling removes a very important check, the courts."

In the decision, Scalia asserted that questions of jurisdiction are so similar to the other issues that trigger Chevron deference that "there is no principled basis for carving out some arbitrary subset of such claims as ‘jurisdictional.’" Scalia added, "Judges should not waste their time in the mental acrobatics needed to decide whether an agency’s interpretation of a statutory provision is ‘jurisdictional’ or non- jurisdictional.’"

Scalia also claimed that those raising the jurisdictional issue under Chevron are actually trying to destroy the Chevron precedent. "Make no mistake – the ultimate target here is Chevron itself," Scalia wrote. "Savvy challengers of agency action would play the jurisdictional card in every case."

Roberts, joined by Justices Anthony Kennedy and Samuel Alito Jr., began his dissent by stating, "My disagreement with the court is fundamental." He asserted that courts, not agencies, have the responsibility of making the threshold determination of the scope of an agency’s authority. "We do not leave it to the agency to decide when it is in charge."

The chief justice continued with a general warning about the growing and unchecked power of the administrative state, which he said "cannot be dismissed." Wrote Roberts, "The citizen confronting thousands of pages of regulations—promulgated by an agency directed by Congress to regulate, say, ‘in the public interest’—can perhaps be excused for thinking that it is the agency really doing the legislating. And with hundreds of federal agencies poking into every nook and cranny of daily life, that citizen might also understandably question whether Presidential oversight—a critical part of the Constitutional plan—is always an effective safeguard against agency overreaching."

In a separate ruling on Monday on attorney’s fees and the National Childhood Vaccine Injury Act, Justice Sonia Sotomayor led the court in holding that attorney’s fees and costs may be awarded to an unsuccessful claimant under the act even if the petition for compensation was untimely. As long as the petition was filed in good faith and there was a reasonable basis for it, wrote Sotomayor, nothing in the act’s text limits fees and costs only to timely petitions.

The decision in Sebelius v. Cloer stemmed from Dr. Melissa Cloer’s petition for compensation, alleging that her multiple sclerosis was caused or exacerbated by the Hepatitis-B vaccine. After her petition was rejected as untimely, she sought attorney’s fees and costs. The justices affirmed the U.S. Court of Appeals for the Federal Circuit.

Also Monday, the court added to its docket a church-state dispute, which up until now has not been a major focus of the Roberts Court. The justices indicated they are ready to revisit one still-controversial issue: invocations before the meetings of government bodies.

The court granted review in Greece v. Galloway, an appeal by the town board of Greece, N.Y. In May 2012, a unanimous three-judge panel of the U.S. Court of Appeals for the Second Circuit ruled against the town’s prayer policy. Judge Guido Calabresi wrote that "a given legislative prayer practice, viewed in its entirety, may not advance a single religious sect."

The case stems from a lawsuit brought by Americans United for Separation of Church and State on behalf of two community residents, Susan Galloway and Linda Stephens. They challenged the board’s practice of inviting clergy to open its meetings with sectarian prayers. Americans United claims that the invocations have been almost always Christian. Rev. Barry W. Lynn, executive director of Americans United, said in a statement on Monday, "Government can’t serve everyone in the community when it endorses one faith over others. That sends the clear message that some are second-class citizens based on what they believe about religion."

The town of Greece, represented by attorneys with Alliance Defending Freedom and counsel of record Thomas Hungar of Gibson, Dunn & Crutcher, contends the justices settled this issue 30 years ago when it upheld the constitutionality of legislative prayers.

"The Founders prayed while drafting our Constitution’s Bill of Rights, and the Supreme Court has ruled that public prayer is part of the ‘history and tradition of this country,’" said David Cortman, senior counsel with the Alliance, in a statement. "America continues this cherished practice."

Tony Mauro can be contacted at tmauro@alm.com. Marcia Coyle can be contacted at mcoyle@alm.com.