A 45-day emergency investigation will examine personnel, medical, mental health, discharge and other policies in all corners of the vast Defense Department. It will also look at ways to improve security and emergency response at Defense Department facilities.
"The shootings at Fort Hood raise a number of troubling questions that demand complete but prompt answers," Gates told a Pentagon news conference.
The quick review will be led by two former Pentagon officials, former Army Secretary Togo West and former Navy chief Vernon Clark.
A longer, second review lasting about six months will look at what Gates called "systemic institutional shortcomings." Gates, who has fired several top officials in three years heading the Pentagon, did not address any possible consequences of the inquiries he announced Thursday.
Gates broached little new information about the case of Army Maj. Nidal Malik Hasan, the Army psychiatrist accused of killing 13 people and wounding more than 30 in the shootings at the Texas military post on Nov. 5.
Gates called it disturbing that Hasan has e-mail contact with a radical cleric in Yemen, but stressed that his review is separate from the criminal investigation into Hasan and should not be interpreted as a finger-pointing exercise against Muslims or anyone else.
Investigators have said e-mails between Hasan and the imam, Anwar al-Awlaki, did not advocate or threaten violence. After the shootings, al-Awlaki's Web site praised Hasan as a hero.
Both Gates and Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, said the chief goal of the Pentagon probe is preventing another such attack and improving future responses by disaster teams.
West was Army secretary in the mid-1990s and later became secretary of veterans affairs. Clark was the chief of naval operations from 2000 to 2005.
In 2007, Gates named West co-chairman of a panel created to review rehabilitation care problems at the Walter Reed Army Medical Center in Washington and the National Naval Medical Center in Bethesda, Md.
In 1995, as President Bill Clinton's Army Secretary, West ordered a review of the Army's racial climate, including whether there were ties between extremist groups and members of the military. The investigation was prompted by the arrests of two paratroopers in connection with the murders of two black people and concerns that the two men may have had ties to white supremacist groups.
Gates would not comment Thursday on whether he considers the Fort Hood attack a terrorist act. Sen. Joseph Lieberman, I-Conn., told a Senate hearing that he does, and urged a government investigation "to learn whether the federal government could have acted in a way that would have prevented these murders from occurring."
Sen. Susan Collins, R-Maine, questioned whether the government failed to connect dots about Hasan.
"We must better understand why law enforcement, intelligence agencies and our military personnel system may have failed in this case," Collins said.
A joint terrorism task force overseen by the FBI learned late last year of Hasan's repeated contact with al-Awlaki, who encouraged Muslims to kill U.S. troops in Iraq. The FBI said the task force did not refer early information about Hasan to superiors because it concluded he wasn't linked to terrorism.
Hasan's psychiatry supervisors at Walter Reed Army Medical Center had expressed concerns in May 2007 about what they described as Hasan's "pattern of poor judgment and lack of professionalism."
President Barack Obama already has ordered a review of all intelligence related to Hasan, including his contacts with al-Awlaki, concerns raised about Hasan by some of his medical colleagues, and whether warnings were properly shared and acted upon within government agencies.
Results of that inquiry are due Nov. 30.