As a reservist Alexis was exempted from the periodic reinvestigation of clearance that active duty officers go through every 4½ years, or the polygraphs they go through every 2½ years.
"We're doing the forensics now to better understand if and how that clearance was reviewed," Kirby said. "If we need to account for missed flags, we will. While not a stellar sailor, nothing Alexis did gave us an indication that he was capable of this brutal level of violence against people."
'Secret' clearance granted in March 2008
Alexis was given a "secret" security clearance in March 2008, shortly after he joined the Navy in 2007.
He carried that clearance with him when he was honorably discharged in 2011, Kirby said, and could use it in another position so long as he is hired within two years.
Alexis was hired by a company called The Experts in September 2012 to work on a HP contract in Japan refreshing computer systems.
"Because he wasn't out of work very long before this next job the security clearance went with him," Kirby said. "We're taking a look at all the run-ins with the law if anything should have been done differently."
The initial background investigation on Alexis was done by the Naval Criminal Investigative Service, Kirby said.
A Defense Department statement issued Tuesday night said "according to applicable federal investigative standards, an individual with Mr. Alexis' non-critical level of eligibility would only need to be reinvestigated once every 10 years."
The Experts issued a statement saying Alexis was properly screened.
"We enlisted a service to perform two background checks, and we confirmed twice through the Department of Defense his Secret government clearance," the statement said. "The latest background check and security clearance confirmation were in late June of 2013 and revealed no issues other than one minor traffic violation."
With security clearance, Alexis worked from September 2012 through January in Japan. His clearance was renewed in July, and he worked at facilities in Rhode Island, North Carolina and Virginia for weeks at a time upgrading computer systems, according to Thomas E. Hoshko, CEO of The Experts. No one reported having any problems with him, Hoshko said.
Alexis began working at the Navy Yard last week, though it was unclear whether he had actually begun doing work or was still securing his base clearance, Hoshko said.
The possible red flags that went unnoticed have members of Congress outraged -- with promises to fix what they say could be gaping holes in the system.
"We are so reliant on military contractors" that the vetting is key to our national security, Sen. Susan Collins told CNN.
Collins, a Republican who serves on the Senate Intelligence Committee, said she now questions "the kind of vetting contractors do."
Washington needs a lot more answers," Rep. Eleanor Holmes Norton, D-District of Columbia, told CNN Tuesday.
Sen. Kelly Ayotte, R-New Hampshire, is asking for a hearing to examine problems the shooting at the Navy Yard highlighted.
"In the wake of this tragedy, we must thoroughly review and fix deficiencies within existing federal contracting hiring practices that the alleged Washington Navy Yard gunman exposed and exploited to ensure the safety of the rest of our service family---servicemembers, civilian workers, and contractors, alike," Ayotte said.
Government relies on contractors
In the 12 years since the September 11 attacks, the United States has ramped up contracting to support new defense and intelligence efforts.
And contractors are a major reason the federal government can operate today as its workforce shrinks.
According to statistics, last year it spent more than $500 billion -- or roughly 14% of the federal budget -- on private-sector contracts.
That doesn't include many contracts awarded by the National Security Agency and other intelligence agencies, which keep their spending classified.