"I can confirm to you that the shooter is in custody and we have a second person detained -- not arrested but has been detained," said Ray Garner, a university spokesman.
Authorities have not yet formally identified the suspected shooter or the detained person.
"As soon as we can go through everything, process the entire scene and also conclude our investigation, at that point, we will be able to give you who the suspects are," Huntsville, Ala., Police Chief Henry Reyes said.
ABC News' Huntsville, Ala., affiliate WAAY-TV reported that the suspect is a university biology professor whose tenure appeal was denied today, though authorities did not publicly confirm the report.
"We're still early in the investigation of this offense," said Charles Gailes, the school's director of public safety, "and I think that anything I say would probably be speculative and would not be good information to the public."
Garner said the three killed were Gopi K. Podila, the chairman of the Department of Biological Sciences, and two other faculty members, Maria Ragland Davis and Adriel Johnson, The Associated Press reported.
The shooting occurred shortly after 4 p.m. local time on the campus at the Shelby Center, a science and engineering building, according to Huntsville Mayor Tommy Battle's chief of staff, Trent Willis.
University and Huntsville police responded to the scene and discovered the victims, Garner said. Authorities then secured and evacuated the building, and conducted additional sweeps.
"This town is not accustomed to shootings and having multiple deaths," Garner said. "I mean, it's a shock to everyone on campus. It's just tragic."
In addition to the dead, three people were injured, two critically, Willis said. All the injured were brought to the Huntsville Hospital.
A third injured person was upgraded Friday evening to fair condition, the AP reported.
The injured were identified as biology department members Luis Cruz-Vera and Joseph Leahy and university staff member Stephanie Monticello, the AP added. It was not clear which of them were injured critically and who was in fair condition.
Erin Johnson, a sophomore at the university, told The Huntsville Times that a biology faculty meeting was under way when she heard "screams coming from the room."
The university Web site carried an "emergency notication" Friday evening telling students that the campus was closed for the evening and that everyone was "encouraged to go home." The message also offered counseling services to students and said, "It has been confirmed no students are involved" in the shooting incident.
Tony Knizer, a sophomore at the school, found it hard to believe such a crime could happen there.
"It's mind-blowing," he told WAAY-TV. "It's making me rethink, like, where I'm safe, you know, and what's going on."
ABC News Radio contributed to this report.