The engineers, conductors and other employees who keep Caltrain running cashed raises totaling nearly 40 percent in the past three years, even as the commuter rail line has been speeding down a path toward fiscal ruin.

The average rank-and-file employee who works for Caltrain earned $68,307 in the fiscal year that ended in September, up from $49,862 three years prior, according to salary data provided by Amtrak, which supplies the workers.

The raises were not the result of extravagance by Caltrain. Rather, they came because Caltrain, under its contract with Amtrak, must pay whatever wages are negotiated between the national railroad and its unions. The negotiations raise Caltrain’s budget even though local officials have no seat at the bargaining table.

The pay hikes are virtually across-the-board, and 80 staffers earned at least $90,000 in the most recent year, up from 15 three years earlier.

In all, Caltrain has paid its work force an additional $5.9 million since 2007 — enough money to keep service running on weekends and during off-peak hours on weekdays. Facing a growing deficit, Caltrain leaders are drafting plans to halt all trains during those periods, leaving only commute-time service as early as late 2011, having recently trimmed the schedule by 12 percent and raised fares.

Some of Caltrain’s 38,000 daily riders between San Francisco and San Jose who were interviewed at the San Mateo station Friday morning said news of the raises was startling as they deal with paying more for less service and combat their own precarious employment situations.

Their most common response: “Are they hiring?”

“I think this is a big sham,” said San Mateo resident Robert Mendez, 45, who depends on Caltrain because a spinal injury prevents him from driving. “That’s a pretty good raise, especially for what they do.”

Unions representing the 400-plus employees — who include everyone from electricians to coach cleaners and maintenance workers — argue they deserved the pay increases and had gone years without salary bumps earlier in the decade.

Amtrak officials said their hands are tied by national labor agreements, and they have virtually no wiggle room to help Caltrain or any individual agency during trying times. And Caltrain defends the contract as an affordable way of doing business.

While their pay has increased much more sharply than their counterparts’ in the Bay Area, their new salaries are not atypical.

Salary increases for line-level employees in the past three years totaled 8 percent at BART and 7 percent at the Santa Clara Valley Transportation Authority. The average BART worker now makes $67,000, while the typical operator at VTA — usually some of the agency’s highest-paid employees — earns $65,000.

How did it happen?

Caltrain administrators in San Carlos oversee the rail line but have contracted the railroad’s operation and maintenance to Amtrak, the nation’s largest such company, since it took over commuter service in 1992.

Caltrain thus bears the brunt of whatever salary deals are struck between Amtrak and its unions. In fact, Caltrain administrators — who have seen their own payroll rise 14 percent in three years — have long said they don’t know what their rank-and-file employees make.

The recent wage increases were almost entirely the result of a new contract reached between powerful, centuries-old U.S. rail unions and Amtrak’s management, based in Washington, D.C.

The unions threatened to strike in 2007 — thereby shutting down the nation’s Amtrak-operated rail lines, including Caltrain — if the employees did not get big pay hikes. But an emergency mediation board appointed by President George W. Bush helped the parties reach an agreement based largely on the government’s recommendation to hand out salary increases similar to what freight railroad workers had already received.

The deal Amtrak and 19 union groups struck in 2008 not only included pay hikes for that year and the next, but also built-in retroactive wage bumps dating back as far as 2002. The Brotherhood of Locomotive Engineers and Trainmen, one of the larger unions, received a 33 percent total hourly wage boost, for instance.

“It really doesn’t matter that it’s Caltrain or Metrolink (in Southern California) or even state-sponsored trains,” they all got the same raises, said Pat Merrill, Amtrak’s western assistant vice president for policy and development. In all, 16,000 employees received salary increases in a contract that cost Amtrak $436 million.

The salary increases for staffers assigned to Caltrain were also due in part to cost-of-living adjustments, changes in work hours and overtime.

Efforts fall short

Merrill said Amtrak has tried to decrease Caltrain’s costs by moving some workers to day shifts and fueling trains in Santa Clara County instead of costlier San Francisco.

“We’re working very closely with (Caltrain) to reduce the contract every time they indicate they need to restructure something,” Merrill said.

But the effort has not done much good. Caltrain’s contract with Amtrak has jumped from $49.3 million in 2007 to $57.9 million in the recently completed fiscal year, even though the amount of work and staff has dropped as the agency has cut service. Employee pay makes up about half the contract and one-third of Caltrain’s total spending.

Defending their pay

The employees and some local union representatives said they are not authorized to talk to reporters, and their bosses at labor headquarters did not return repeated calls for comment. But those who agreed to speak on the condition of anonymity defended the pay hike.

“We’re still (in the) lower tier as far as various railroads across the country, as far as pay rate goes,” one veteran Caltrain conductor said. “When (increased) medical expenses are factored into it, our raise was extremely minimal.”

Union officials blamed Caltrain’s financial problems on other factors, such as state and local cuts — which, along with falling ridership and the salary increases, have led to the budget woes.

“If you go without a wage increase for (a while) and finally get one, it’s going to be a big one. That’s the bottom line,” a local union rep said. “I didn’t get a pay increase for the entire Bush administration.”

Another union official, when asked if the employees deserved the wage hike, said: “Everybody deserves a pay increase, don’t they?”

Future unknown

Caltrain public affairs chief Mark Simon said contracting is common practice for train lines — Amtrak provides service for three other U.S. commuter agencies — particularly because the work is highly specialized.

“It certainly is cheaper than hiring an entire railroad operation staff, I think we can safely say,” Simon said.

Still, the current contract, signed in November 2001, will expire at the end of June. Amtrak has applied to keep control of the service, and Caltrain said it has received “multiple” competing offers.

“We think Amtrak’s worked out well as our contractor, but we’re happy to be going to the market,” Simon said.

Mike Rosenberg covers San Mateo, Burlingame, Belmont and transportation. Contact him at 650-348-4324.