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Caltrain is facing a potential $30 million deficit, which would result in drastic service cuts if current trends continue, according to agency officials.

As the commuter-rail agency between San Francisco and San Mateo and Santa Clara counties begins its next budget process, cuts could be as severe as a reduction in service to 48 trains that would operate only during weekday commute hours, Caltrain officials said in a prepared statement.

Other services that might be eliminated include weekday service outside the commute peak, weekend service and service south of the San Jose Diridon station. Service also could be suspended at up to seven stations.

"We are not saying that this is what we are going to do, or where we are going to end up," said Mark Simon, executive officer for public affairs. "But this is where we are starting."

Caltrain is the only San Francisco Bay-area transit system that operates without a permanent, dedicated funding source, such as a sales tax, Caltrain officials said. To balance its budget, Caltrain relies on contributions from partner agencies: the city and county of San Francisco, San Mateo County Transit District (SamTrans) and the Santa Clara Valley Transportation Authority.

In fiscal-year 2011, contributions from the partner agencies made up about 34 percent of Caltrain’s operating budget; fares accounted for about 44 percent.

SamTrans is expected to reduce its annual contribution to Caltrain by about $4.7 million. If  other agencies do the same, Caltrain’s budget shortfall would reach about $30 million, Caltrain officials said.

Caltrain currently operates 86 weekday trains, including 22 express trains, with an average ridership of 40,000. Saturday service includes 32 local trains and four express trains; Sunday service includes 28 trains and four express trains.