Investigators did not say whether the gunman killed himself or was killed by someone else. They also did not provide any details on the victim or the gunman or provide a possible motive for the shooting.
Fort Bliss Maj. Gen. Stephen M. Twitty said the shooting happened at the El Paso Veterans Affairs Health Care System's clinic, which is in a complex that includes the William Beaumont Army Medical Center. The entire complex was locked down Tuesday as authorities responded to the shooting.
"The alleged shooter is dead, and we have one casualty. That casualty is deceased. All other VA patients and staff are safe," said Twitty, commanding officer of nearby Fort Bliss.
"Everything is under control and there is no immediate threat to Fort Bliss or the local community," Twitty said at a news conference Tuesday night.
The VA clinic will be closed Wednesday, said its acting director, Peter Dancy.
The FBI, which is leading the investigation, has hundreds of potential witnesses, many of whom were patients or would-be patients at the clinic, said Douglas Lindquist, special agent in charge of the FBI El Paso office.
"Those people were here seeking medical assistance, so we understand the difficulties that this situation presents to them and we're trying to expeditiously get through those hundreds of witnesses to find out details about this incident," Lindquist said.
The VA clinic came under scrutiny last year after a federal audit showed it had some of the nation's longest wait times for veterans' trying to see a doctor for the first time. A survey of hundreds of West Texas veterans last year found that they waited an average of more than two months to see a Veterans Affairs mental health professional and even longer to see a physician.
U.S. Rep. Beto O'Rourke commissioned that survey of more than 690 veterans living in El Paso County. O'Rourke also was active in a congressional probe into long waiting times in the VA health care system.
In a statement issued by his office Tuesday, the El Paso Democrat said his "thoughts and prayers are with the men and women at the El Paso VA clinic."
The VA said in a statement that it "is deeply saddened by the tragic situation that has occurred in El Paso, and we are actively working with our partners at Fort Bliss to investigate this matter."
"The safety and continued care of our veterans and the staff will be our focus throughout this situation," the agency said.