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(The following story by Thomas Frank appeared on the USA Today website on January 28, 2009.)

WASHINGTON — The first federal evaluation of mass-transit security shows that more than 75% of the nation’s major rail and bus systems aren’t meeting Homeland Security guidelines.

By contrast, 96% of airlines are complying with security requirements, according to a new report by the department. The report doesn’t identify which rail and bus systems fell short.

The assessment comes as new Homeland Security Secretary Janet Napolitano says she plans to focus more on mass transit, possibly through “redeployment” of resources from other areas.

“We’ve done an awful lot in the aviation world,” Napolitano said Monday. “We could pay more attention” to surface transportation security.

The department’s little-noticed evaluation, published on its website Jan. 15 just before Napolitano took office, found that 37 of the nation’s 48 largest transit systems aren’t complying with voluntary guidelines set in 2007. There is no sanction for non-compliance, said Paul Lennon, head of mass transit for the Transportation Security Administration (TSA).

Guidelines include training transit workers in security, running security drills regularly and sharing intelligence with other agencies.

“The threat is clearly real. Terrorists go after public-transportation systems,” said Brian Jenkins, director of the National Transportation Security Center of Excellence at San Jose State University.

Jenkins said major systems in cities such as New York and Washington have vastly improved security while smaller agencies “may not see this with the same degree of urgency.” A 2007 report by the Department of Transportation found that smaller transit agencies “consider themselves to be unlikely targets for terrorist attacks.”

The recent Homeland Security evaluation includes bus systems in the suburbs of Chicago and New York, and bus and light-rail systems in Buffalo, St. Louis and Sacramento. Such smaller systems might be appealing targets for “homegrown” terrorists who “operate fairly close to home,” Jenkins said.

“The industry knows it has difficulty fully complying with guidelines,” said Greg Hull, security director for the American Public Transportation Association. Transit agencies need more federal money to pay for training, access-control systems and other security improvements, Hull said.

Lennon of the TSA said all transit agencies have improved security since 9/11 and comply with many but not all of the guidelines.

Some Homeland Security recommendations involve planning and could be done at little or no cost, Jenkins said.