Flowers, a redshirt junior from Los Angeles, was 21. The cause of death was not released.
"Earlier this morning we were made aware of the tragic loss of Nahje Flowers," New Mexico coach Bob Davie said in a statement. "Our entire football team and everyone who knew Nahje are devastated by this loss. Nahje was a wonderful person and great teammate. Our entire Lobo Football family mourns his passing and our prayers go out to his family."
Davie met with the team early Tuesday morning and grief counselors and a psychologist will be made available, according to New Mexico athletic director Eddie Nuñez.
"Our focus right now is on the well-being of our student-athletes, coaches and staff and the support needed," Nuñez said in a statement. "Nahje was an incredible young man. Our entire Lobo Football family mourns his passing, and our prayers go out to his family."
Flowers attended Dorsey High in Los Angeles, where he also participated in wrestling and track and field.
He appeared in five games for the Lobos this season, tallying 13 total tackles and 1.5 sacks.