The two agencies responsible for building the Peninsula section of the high-speed-rail system now find themselves in a competitive race for federal-stimulus funds, Caltrain's chief spokesman told the Palo Alto City Council Monday night.

Mark Simon, Caltrain's executive officer for public affairs, asked the council to support Caltrain's proposed amendments to Senate Bill 965, a bill that governs expenditure of the American Recovery and Reinvestment Act funds.

Simon said Caltrain hopes the amendments would allow it to obtain some of this federal money and, in doing so, fund rail improvements on the Peninsula.

"Part of the concern is if we don't speak up for this money now it will go to another segment somewhere else in the state," Simon told the council.

Simon said he expects the rail authority, which is banking on the federal funds, to oppose the Caltrain amendments.

Caltrain and the rail authority are both seeking to secure major portions of the $2.25 billion the federal government allotted to California in January for high-speed rail. The two agencies signed a memorandum of understanding last year to work together on the Peninsula segment of the controversial high-speed-rail line, which has attracted waves of opposition in Palo Alto and around the Peninsula.

The rail authority has yet to complete the required environmental analysis for the Bay Area segment of the line and could lose the federal grant if the analysis isn't completed by November 2011.

Caltrain's project, by contrast, has already undergone the required reviews and could be implemented as soon as the cash-strapped agency finds the $1.5 billion required to fund it.

Under the rail authority's current plan, the new high-speed-rail line would share the Caltrain corridor with Caltrain on San Francisco-to-San Jose segment. The authority has not yet determined how these two systems would share the corridor, which is owned by Caltrain.

The race for federal funds could create a fissure between Caltrain and the rail authority, the two agencies that united last year to form the Peninsula Rail Program.

"It's a true partnership, which means you don't always get along," Simon said. "You indicate things you disagree over and, hopefully, you can work these out and move forward."

He said Caltrain is not looking to abandon its partnership with the rail authority, but said the agency would only be willing to share its right-of-way if the new rail line doesn't hinder existing rail service. He said Caltrain partnered with the authority in hopes of finding a way to pay for the electrification process.

"When the partnership doesn't work for us, we're prepared to assert our ownership rights of the right of way," Simon said.

The rail authority has assumed in its business plan that the entire federal amount would be used to fund voter-approved high-speed-rail project -- an 800-mile system between San Francisco and Los Angeles that the authority plans to have in place by 2020. The rail authority estimates the project to cost about $43 billion and, according to its most recent business plan, is banking on about $17 billion in federal grants for the project.

But on Monday night, Simon told the council that Caltrain hopes to use the federal funds for its own project -- the long-planned electrification of the Caltrain -- and asked the council to support Caltrain's bid for federal funds.

If delays in the Bay Area high-speed-rail segment continue and the first round of federal funding is reallocated elsewhere, the likeliest destination could be the Anaheim segment of the line, which has made the furthest progress toward environmental clearance. It doesn't hurt that Curt Pringle, the chairman of the rail authority's board of directors, is the Anaheim mayor, Simon said.

Simon's presentation came at a time when the council was discussing the revised "guiding principles" for its High-Speed Rail Committee. The principles, which the council adopted unanimously, reinforce Palo Alto's opposition to elevated high-speed-rail alignment. They also allege that the rail authority's ridership study "contains dubious and erroneous assumptions" and that its pending environmental review for the Central Valley-to-San Francisco segment is "fatally flawed."

Vice Mayor Sid Espinosa praised the new guiding principles as a document that "puts a stake in the ground" and clearly establishes Palo Alto's position on major high-speed-rail issues. The new principles also state that Palo Alto "strongly supports" Caltrain and its electrification project, "independent of high-speed rail."

The council generally expressed support for Caltrain's proposed legislative amendments and agreed to discuss the issue further and, if needed, pass a resolution supporting Caltrain's effort.

The council's High-Speed Rail Committee is scheduled to discuss Caltrain's amendments to SB 965 at its meeting Thursday morning. The full council would vote on the proposed resolution at its May 24 meeting.