"The exemptions allow the university to legally uphold its longstanding rights as a religious university," said Brett Crandall, a spokesman for BYU-Idaho, in a prepared statement.
Title IX was a 1972 act of Congress designed to prevent discrimination on the basis of sex, which the department later expanded to include gender identity. Under the law, schools that receive federal funding should ensure equal treatment, regardless of a person's gender identity, sexual orientation, marital status or whether a woman has had an abortion.
But the private Idaho school of 16,000 students has had permission since the 1980s to disregard certain elements on the basis that they are inconsistent with the Mormon faith.
Federal officials' March decision allows the private school to consider a person's gender identity in admissions, school activities and housing, as well as counseling and health services.
Religious immunities granted to about 130 faith-based colleges nationwide have drawn ire from activists who say they tacitly endorse unfair treatment of gay and transgender students and staff.
This is "extremely hurtful and harmful to LGBT youth," said Shane Windmeyer, executive director of North Carolina-based organization Campus Pride.
Crandall said Gilbert was not available for comment Friday. The school president detailed his request for an exemption in a Feb. 12 letter to Catherine Lhamon, the assistant secretary for civil rights at the U.S. Department of Education.
"BYU-Idaho shares and supports the goal of the Office for Civil Rights to eliminate sex discrimination," Gilbert maintained. However, according to LDS teachings, "gender is not simply socially determined but is an essential characteristic of each person's eternal identity."
Clark noted the school's mandatory Honor Code compact forbids premarital sex and enforces modest dress. It also prohibits adopting a new gender identity or engaging in same-sex relationships.
BYU's campuses in Provo and Hawaii have a mandatory Honor Code, but neither campus has received a religious waiver from protecting transgender students, according to federal officials.
The education department on Friday released an updated list of colleges with exemptions granted since 2009, though BYU's Idaho campus was inadvertently left off that list, a spokeswoman said.
In 1985 and 1988, when it was known as Ricks College, BYU-Idaho received waivers that allowed the school to consider marital and parental status of students and employees, and it exempted its health insurance from covering pregnancy-related conditions for unmarried women. BYU's Provo and Hawaii campuses received similar allowances around the same time.
Windmeyer maintains any exemption is harmful to students.
"In today's society, regardless of your religious values," he said, "no one wants to send their kid to a campus that's not a safe, welcoming place for all people."