Amtrak’s top executive warned Congress that a mandate requiring federal employees to be vaccinated would result in reduced service, a problem that could affect long-distance train travel in the U.S.

Amtrak president Stephen Gardner said about 5% of its total workforce of 18,000 — roughly 900 employees — have yet to get vaccinated. The deadline for federal employees under a new mandate is Jan. 4.

“We anticipate proactively needing to temporarily reduce some train frequencies across our network in January to avoid staffing related cancellations, with our plan to fully restore all frequencies by March or as soon as we have qualified employees available,” Gardner said at a hearing before the transportation committee Thursday.

Gardner said those reductions are likely to be felt on Amtrak’s long-distance routes, where small crews of conductors and engineers are deployed to work at intermediate points along a train’s path. In Massachusetts, that includes the Lake Shore Limited, a 19-hour route traveling between New York, Boston and Chicago.

Sean Jeans-Gail, vice president of government affairs for the Rail Passengers Association, a Washington advocacy group, said it’s hard predict where the reductions could occur, but he said they're more likely to be in Republican-led states where vaccination rates tend to be lower, and not in the Northeast.

“What we are advocating to Congress and to Amtrak is that we be as surgical in applying these cuts as possible,” Jeans-Gail said. “I would say Massachusetts would be at the very low end of the distribution curve on how it is affected.”

Amtrak’s shorter routes in the Northeast Corridor between Boston, New York and Washington are unlikely to be affected because they travel through densely populated areas and have crew redundancies that can step in for employees who are terminated due to failure to comply with the vaccine mandate.

Still, staffing shortages could have an impact on the region's busy commuter corridor.

Jarred Johnson, chief operating officer and development director for TransitMatters, a local transportation advocacy group, noted that many short-haul flights between Boston and neighboring cities have been taken over by rail service.

"At this juncture, we should really be replacing more of our trips to New York and Portland less by car, by plane, but by train," he said. "This is certainly not going to help that effort."

President Joe Biden issued an executive order on Sept. 9 requiring federal contractors and subcontractors to comply with workplace safety guidelines developed by a federal task force. That task force subsequently issued guidelines that new, renewed or extended contracts include a clause requiring employees to be fully vaccinated by Jan. 18. That means those receiving a two-dose vaccine must get their second shot by Jan. 4.

Some Republican-led states have pushed back against the mandate. Earlier this week, a federal judge in Georgia blocked the Biden administration from enforcing a COVID-19 vaccine mandate for employees of federal contractors in the construction industry.

Amtrak has also laid off or furloughed engineers, conductors and other employees since the start of the pandemic due to steep declines in ridership. The agency is operating around 80% of its pre-pandemic schedules and is now facing pressure to bring employees back or out of retirement. Jeans-Gail said it can take three months to a year to train new conductors and engineers.

The route reductions and expected employee shortages are also taking place as Congress begins to implement a landmark infrastructure bill that puts $66 billion into rail modernization and expanded intercity service.