The Virginia Railway Express has been notified that it may not receive about $10 million in state transportation funding, a development that could mean steep increases in passenger fares.

VRE, which serves about 20,000 riders daily on its lines from Fredericksburg and Manassas, was told in a letter from the state that $9.6 million in transportation funding expected from the federal government may not be coming this year. The annual allocation is generally used to pay “track access fees” charged by the CSX and Norfolk Southern rail lines.

News of the funding issue came to public light Friday at a meeting of VRE’s operations board.

The federal money typically comes through the Virginia Department of Rail and Public Transportation, officials said. But officials were notified that because of how federal dollars were allocated this year, the rail agency no longer has the funds available.

“This is a very serious issue to our budget,” said Doug Allen, chief executive of VRE.

While the money did not come through state rail agency as it usually does, the funds are elsewhere in the budget of the Virginia Department of Transportation. VDOT is controlled by the Commonwealth Transportation Board and led by Sean T. Connaughton, the state’s transportation secretary.

Federal legislation eliminated the traditional source of funding the fees, Connaughton said in an e-mail. “The Commonwealth will work with VRE to find a new source of paying for track access,” he said.

To ensure that happens, VRE spokesman Mark Roeber said, the agency will lobby Gov. Robert F. McDonnell (R), the General Assembly and the Commonwealth Transportation Board.

If the $9.6 million in funding is not supplied by the state, officials say they would face several options: reducing service; asking the local jurisdictions that control VRE to make up the shortfall; or increasing fares by as much as 28 percent.

A monthly ticket for travel between Manassas and Union Station costs $241. It would jump to $308 if VRE chose to cover the shortfall exclusively through a fare increase.

Manassas City Council member Jonathan Way (R) said that VRE shouldn’t push the panic button yet because the funds could be restored by Connaughton or the Commonwealth Transportation Board.

“This may be a ghost as opposed to a real problem,” Way said.

Fairfax County Board of Supervisor Chairman Sharon Bulova (D) said that VRE’s message to the state is simple: “We hope that money will be directed, as it always has been, to the VRE.”