Mayor Eric Adams on Tuesday decried the separation of church and state, while also praising prayer in schools — raising eyebrows and the ire of civil libertarians.

The mayor, who has previously made no secret of his personal religious values, made his pitch for a more spiritual Big Apple at an annual breakfast of faith-based leaders in Manhattan.

“Don’t tell me about no separation of church and state. State is the body. Church is the heart. You take the heart out of the body, the body dies,’’ Adams said.

“I can’t separate my belief because I’m an elected official. When I walk, I walk with God. When I talk, I talk with God. When I put policies in place, I put them in with a God-like approach to them. That’s who I am.”

The mayor told the audience at the New York Public Library’s main branch that a lack of faith can be linked to everything from homelessness to domestic violence to guns in schools.

“When we took prayers out of schools, guns came into schools,’’ Hizzoner said.

The Bill of Rights guarantees the separation of Church and State, and requiring prayer in public schools was outlawed in 1962.

Adams’ comments immediately came under fire from some civil-liberty activists.

“In order for our government to truly represent us, it must not favor any belief over another, including non-belief,’’ the New York Civil Liberties Union tweeted along with a press statement criticizing the mayor.

“On matters of faith, the Mayor is entitled to his own beliefs. On the Constitution, he must uphold his oath.”

NYCLU President Donna Lieberman added in the statement, “It is odd that Mayor Adams would need a refresher course on the First Amendment.

“After all, he has sworn to uphold the Constitution more than once, first as a police officer, later as a state representative, and then last year upon becoming mayor,’’ she said.

Naomi Paiss, the former head of Americans United for Separation of Church and State, added on Twitter, “So much for blue-city mayors upholding a fundamental principle of American society.”

Meanwhile, Adams said it is a “Shakespearean tragedy’’ when city residents don’t explore and appreciate the Big Apple.

“When I walk into a Sikh temple or sit down at a Sukkah or go into a Diwali celebration, do you know how many people in this city have never left the geographical boundaries of the neighborhood they live in and the geographical boundaries of their mindset?’’ Adams said.

“They only know people that look like them, talk like them, eat the same food, do the same things. That is a Shakespearean tragedy and anti-Christopher Columbus theory, believing if you leave your intellectual thought process, you’re going to fall off some type of globe or planet.

“No, expand the beauty of this diversity.’’

– Additional reporting by Bernadette Hogan