Caltrain has gone broke and will likely need to wipe out half its service — including weekend, nighttime and midday trains — officials warned Thursday, bracing passengers for a major shake-up to the popular commuter line that links San Francisco to the South Bay.

“This is not an April Fools’ joke,” Caltrain CEO Mike Scanlon told the agency’s board of directors. “This is real. We’re at a watershed moment where there’s a possibility this railroad could go away.”

Scanlon said the service cuts, which would idle trains for much of the day, would need to be completed by June 2011, although the agency may begin slashing its schedule as soon as this fall.

The train line is falling victim to a combination of declining revenues from state and local agencies and falling ridership. Although officials expect a passionate outcry from riders who depend on Caltrain, they insisted the dire warnings aren’t a ploy to justify more fee increases or tax hikes.

The cuts would hamper those who rely on Caltrain to get to work during odd hours, prevent most service to special events such as San Francisco Giants and San Jose Sharks games, and leave cities planning dense developments near train stations in the lurch.

The cuts would affect an average of 18,211 weekend riders, 5,718 midday riders and 2,082 nighttime riders, officials said.

Caltrain’s board, needing to slice about $30 million from its $97 million budget, will vote on specific proposals at a future meeting after holding public hearings.

Caltrain officials said the service cuts will further jam traffic on roadways. The majority of Caltrain’s 40,000 daily passengers ride during commute times, and much of that service may remain untouched because it is the most profitable.

But Caltrain also runs hourly service that stops at every station on weekends, plus on weekdays from 10 a.m. to 2 p.m. and after 8 p.m. Those trains, including 32 on Saturday and 28 on Sunday, are facing elimination.

John Murphy rides Caltrain from San Francisco to work in Santa Clara, balancing the commute with taking care of his young son. He said the midday cuts would be “horrible” and would force him and his wife to buy a second car, move closer to his office or switch jobs.

“All the jobs I can do are down here” in Silicon Valley, Murphy said. “My wife is in marketing — all her jobs are up (in San Francisco). Caltrain makes it work.”

Caltrain’s financial state has long been declining, and officials trimmed the weekday schedule from 98 to 90 trains in August and hiked fares in early 2009.

The agency has lost $10 million in funding from the state each of the past three years. And for more than a year, it has been losing riders, which account for 40 percent of its revenue.

But now a new, more damaging problem has emerged. Scanlon, who is also the CEO of the San Mateo County Transit District, or SamTrans, said he will ask that agency’s board of directors to lower its Caltrain contribution by nearly 70 percent by July 2011.

SamTrans, the Santa Clara Valley Transportation Authority and San Francisco Muni each provide Caltrain with a subsidy, which combined amounts to $39.4 million. But with the smaller SamTrans contribution, VTA and Muni will lower their shares proportionately. SamTrans, Muni and VTA all recently cut service and raised fares, and Scanlon said they are “beyond broke.”

A fare increase has not been proposed, as officials say it would drive away even more riders. They also don’t expect to propose any ballot measures, such as tax increases, citing the recession.

As part of the service cuts, some employees would lose their jobs, although officials are not sure how many.

It costs $60.4 million per year to run the railroad, plus another $13.8 million for fuel and $9.9 million for administration. The agency spends the remaining $11.9 million on shuttles, insurance, maintenance, utilities and other services.

Officials stopped short of saying they expected to close the railroad, which has been open since 1863 and carrying passengers since 1904, but said the news calls into question the operator’s ability to survive. Scanlon said the agency’s business model is simply not sustainable.

“We’re rapidly approaching a cliff,” he said. “It’s going to be very, very painful. It’s probably going to force people back to congested freeways. People aren’t going to be able to get to jobs; they’re not going to have basic mobility.”

Scanlon said there are some long-shot possibilities for more money — such as the reinstatement of state transit assistance or help from the Bay Area Metropolitan Transportation Commission. But he said it would have to be a yearly commitment from a government during a climate in which they are all spending less.

“I don’t see any silver bullets,” he said.

At the Caltrain station in Santa Clara on Thursday afternoon, those waiting to ride the train weren’t happy to hear the news.

“Can’t we do something about this?” asked Alyssa Salcido, a 20-year-old Santa Clara University student. “I know a ton of students who (use Caltrain to) go into the city to see a play or have dinner or go to the games. I’m not for this at all.”

Salcido, who does not have a car, said she rides Caltrain to visit her siblings in San Francisco. Without Caltrain, “How am I going to get there, fly?”

Anna Koster of Santa Clara had a similar reaction.

“Oh my God, that would be terrible,” Koster said. “It looks like I could just get to and from work, but could never get sick and leave early or stay really late. I also use Caltrain to go to San Francisco on the weekends, and that would be out.”

Bay Area News Group staff writers Lisa Fernandez and Gary Richards contributed to this report. Contact Mike Rosenberg at 650-348-4324.