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Caltrain’s CEO, who has proposed shutting half the rail line’s stations and halting much of its service to survive financially, earns more than $400,000 in salary — more than any transit boss in California.

Last year, Caltrain chief Mike Scanlon took home 59 percent more than the median salary for a CEO of one of the state’s 23 largest transit operators, according to a Bay Area News Group review of salaries released by the State Controller’s Office this month.

Scanlon’s pay topped the list even though the three agencies he oversees — Caltrain, SamTrans and the San Mateo County Transportation Authority — are average in size when combined and are on far shakier ground financially than most other transit operators. And he’s not the only one who has seen a hefty bump in pay at Caltrain, where both administrators and train workers have enjoyed pay raises in recent years.

“Good personnel come at a high price,” said Mike Nevin, a former Caltrain and SamTrans board chairman who led the search committee that found Scanlon. “I realize it’s expensive, but I feel he’s the best.”

Scanlon’s $400,668 salary eclipsed the second-best-paid transit chief, BART General Manager Dorothy Dugger, by $47,000, even though BART has four times more employees and riders. And Scanlon made $137,000 more than the chief of the state’s largest transit agency, Los Angeles Metro, which is about 15 times bigger.

Michael Burns, general manager of the Santa

Clara Valley Transportation Authority, made $291,192 in 2009, and turned down a bonus because of the agency’s budget struggles, his spokeswoman said.

Scanlon declined to comment on his compensation, which totals nearly $440,000 including benefits.

Defending his pay

The 44-year industry veteran has collected plenty of supporters since taking the job in 1999. His peers recently named him chairman of

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