A deputy attorney general in Texas Attorney General Ken Paxton's office says a Frisco school's prayer room may violate the First Amendment's protection of religious liberty.

In a letter to Jeremy Lyon, superintendent of the Frisco Independent School District, Deputy Attorney General Andrew Leonie urged neutrality toward all religions in response to complaints that Liberty High School's prayer room excluded non-Muslim students.

"It appears that students are being treated different based on their religious beliefs," said the letter. "Such a practice, of course, is irreconcilable with our nation's enduring commitment to religious liberty."

Leonie encouraged the environment of free religious practice, but warned against favoring one religion over another.

"I ask that you ensure that Liberty High School's prayer room is accessible to students of all religious denominations, consistent with the First Amendment's protection of religious liberty," said Leonie.

The letter was included in a press release sent to media outlets Friday.

Frisco ISD spokesperson Chris Moore said the district first learned about Leonie's concerns through calls from the media.

In a written response to Leonie on Friday afternoon, Lyon said the press release "appears to be a publicity stunt by the OAG to politicize a non-issue."

Earlier this month, the prayer room was featured in a news report by a student journalist at Liberty High School.

The video shows Muslim students praying in a classroom Moore says would otherwise be empty at that time.

"It gives us a way to like pray in our classrooms and then go straight back to class," said junior Sarah Qureshi, in the video published by Liberty Wingspan.

The process of praying during the day used to take more than an hour, the district says.

Muslims are required to pray five times a day.

Students used to have to leave school and go to a mosque until the prayer room was started in 2009.

"I think it is a really great opportunity," Qureshi said in the video.

The concern by the Attorney General's Office is that the room is dedicated to students of the Muslim faith and that it isn't available to students of other religions.

Moore says the prayer room is open to each of the schools 2,100 students.

"It's not just a room for Muslim students. It's a room Buddhist students, Jewish students, Catholic students, Hindu students, anyone who wants to use that room in that capacity can," Moore said.

Moore said he isn't sure why the Attorney General's Office would bring up the concerns publicly without contacting them first.

He says the district is eager to clarify its position.

In the meantime, the prayer room will remain open.

Liberty High School isn't the only Frisco school with a prayer room. Heritage High School has one as well.

See the full text of the letter below.

NBC 5's Jennifer Phillips contributed to this report.