WASHINGTON - When Aaron Alexis received an access card to enter the Washington Navy Yard, the Pentagon relied on a 5-year-old background investigation completed before most of his brushes with police and signs of mental illness, a senior Defense Department official said Wednesday.

But the 2008 investigation was considered recent enough under federal rules for Alexis to be granted permission to enter the Navy Yard, where he worked, merely by flashing his card to a guard at the gate.

Monday's shooting rampage, in which Alexis killed 12 people before police shot him dead, has raised questions about how the troubled computer contractor was able to keep a secret-level security clearance.

The answer appears to be simple but troubling: The government relies mostly on the honor system - or blind luck - to keep tabs on many of the 4.9 million people who hold security clearances.

If an employee of a Pentagon contractor is arrested or exhibits mental problems, the company is supposed to report the incidents to the Defense Department, officials said. But doing so could result in the person's clearance being revoked, rendering him useless to work on classified government contracts.

A senior U.S. official said the government checked to ensure that companies complied with requirements to disclose information about employees that could result in lost security clearances. But the number of people holding clearances makes it impossible to monitor every pass holder closely enough to detect those here in trouble, officials and outside experts say.

The federal government is looking at ways to create a system in which agencies would receive automatic notifications when people with security clearances are arrested or involved in an incident that could jeopardize their clearance.

The Navy Yard shooting is the second major incident this year that has created questions about the efficacy of the government's system of security clearances for contract workers. This spring, National Security Agency contractor Edward Snowden leaked a large number of classified documents to news organizations. Although the two cases differ widely, both have prompted calls to reform the system.

Some experts warn, however, that the government's response to the Navy Yard rampage could lengthen the delays that already frustrate many with a legitimate need for a security clearance.

"There's always a pendulum swing in response to the latest incident," said Steven Aftergood, an expert in classified procedures with the Federation of American Scientists. "Finding the optimum balance between security and productivity is a tricky matter that can't be prescribed by regulation."

As for Alexis, he underwent the months-long process of getting a security clearance after joining the Navy in 2007. The background investigation by the federal Office of Personnel Management required him to fill out a lengthy form asking about many aspects of his life, including arrests, foreign travel, loyalty to the U.S. government and whether he had ever sought mental health counseling.

The personnel office relies heavily on contractors to process and double-check the thousands of background investigations it handles every month. In 2008, after the background check was complete, he received a clearance at the "secret" level, valid for 10 years.

Although most details about this initial investigation into Alexis' past remain unknown, one official said investigators probably were aware of his 2004 arrest in Seattle after he shot out the tires of a construction vehicle in what he described to police as an anger-fueled blackout.

Navy officials said Wednesday they knew about Alexis' arrest when he enlisted but decided it did not disqualify him since he was neither charged nor convicted of a crime.

A "secret" clearance is a relatively low level, requiring nothing close to the scrutiny that comes with "top secret" or higher.

Holding onto a secret clearance is also easier. While still in the Navy, Alexis was able to keep it despite a 2008 arrest for disorderly conduct in Georgia after being thrown out of a bar at 1 a.m. Navy officials said he had disciplinary problems, but because he was not convicted of any crime he was not in danger of losing his security clearance.

When he left the service in early 2011, his clearance became inactive. But under government rules, he could get it reactivated without undergoing another investigation as long as he took a job requiring a security clearance within two years.

In 2012, when Alexis went to work for the Experts, a computer consulting company, his clearance was restored. The company did a background check on him in July that turned up no issues, according to Thomas E. Hoshko, chief executive officer of the Experts. Even in recent months, when the company received calls from Alexis indicating potential trouble, none triggered an alarm.

Alexis "performed well and was a good worker," said Lou Colasuonno, a spokesman for the Experts.

Questions about his conduct "never rose to the level where it needed to be reported," he said.

david.cloud@latimes.com