Justice Samuel A. Alito Jr. warned on Saturday that freedom of speech was under threat at universities and that freedom of religion was in peril in society at large.

“Troubled waters are slamming against some of our most fundamental principles,” he said.

He made his remarks at a commencement ceremony at the Franciscan University of Steubenville in Ohio, a Catholic institution.

“Support for freedom of speech is declining dangerously, especially where it should find deepest acceptance,” he said.

A university, he said, should be “a place for reasoned debate.” But he added that “today, very few colleges live up to that ideal.”

The same is true, he said, for tolerance of religious views in society generally.

“Freedom of religion is also imperiled,” he said. “When you venture out into the world, you may well find yourself in a job or a community or a social setting when you will be pressured to endorse ideas you don’t believe or to abandon core beliefs. It will be up to you to stand firm.”

In other settings, Justice Alito has given a specific example, complaining that people opposed to same-sex marriage on religious grounds are sometimes treated as bigots.