A proposed agreement between the agency overseeing Caltrain and the one responsible for building the new high-speed rail line has Palo Alto officials worried that the controversial project is moving too fast and in the wrong direction.

The draft memorandum of understanding between the Peninsula Corridor Joint Powers Board and the California High-Speed Rail Authority lays out the framework for cooperation between the two agencies. But the document also indicates that the two agencies already have a fairly clear idea of what the Caltrain corridor would look like when the high-speed rail is built.

"Ultimate configuration of the Caltrain corridor will be a four-track, grade-separated high speed rail system, with mixed traffic from Caltrain commuter rail and the high speed train service capable of operation on all four tracks to enable Caltrain to achieve service levels of no less than eight trains per hour in each direction," the agreement between the two agencies reads. "In some places, the corridor may consist of more than four tracks."

The statement appears to contradict earlier assertions by rail-authority officials that all design options -- including running the high-speed rail through an underground tunnel -- are still on the table. Palo Alto officials and residents have strongly argued that running the line underground would be in the best interests of the city. Residents in the Southgate neighborhood, adjacent to the Caltrain corridor, have been particularly vehement in criticizing the above-ground alternative, which could require the rail authority to seize their properties through eminent domain in order to widen the rail right-of-way.

In the next week, the city plans to send a letter to the rail authority, asking the agency to study design options other than elevated tracks along the Caltrain corridor. Councilman Pat Burt, who is a member of a recently formed council subcommittee focusing on the high-speed rail, said the section of the memorandum describing the track design "stuck out like a sore thumb."

Burt said he was concerned about the contradictory statements from rail authority officials, who have long presented the four-track design as one of several that would be considered. As recently as March 2, Rod Diridon, member of the rail authority's board of directors, told the council that the agency would consider every viable option.

"We're going to look at every alternative that was brought before us," Diridon told the council. "We'll do a thorough evaluation of every one of those alternatives."

Diridon also indicated in October -- one month before California voters approved a $9.95 billion bond measure for the project -- that Palo Alto staff would be involved in the decision-making process, which will involve a wide range of alternatives, including two-track systems and four-track systems.

"All of those will have to be examined," Diridon told the council in October. "Whether (the trains) will be in a tunnel, in a trench covered, in a trench open, whether they'd be on-grade and elevated would be studied."

"Your staff would be deeply involved in that," he added.

At that time, eight councilmembers voted to support Proposition 1A, which provided the funds for the San Francisco to Los Angeles rail system (Yiaway Yeh was absent). But even at that time, Councilman Greg Schmid warned that an above-ground line could hurt the community and made it clear that he was only supporting the proposition because of the possibility of running the rail underground.

"I think of high-speed rail lines going down the Peninsula and dividing the communities the way rivers used to divide communities in the Middle Ages," Councilman Greg Schmid said at the October meeting. "It's not necessarily in our interests to have this division take place in an area where the networking of ideas is the key to success."

But now, some council members are worried that the rail authority has already made its decision without any consultation. Burt said he was concerned about the inclusion of the four-track design in the memorandum between the two agencies.

"We thought it was inappropriate," Burt said Friday. "It's a cart getting ahead of the horse."

Council member Yoriko Kishimoto, another member of the high-speed-rail subcommittee, also said she was concerned about the wording of the memorandum. Kishimoto has recently organized a coalition of Peninsula cities that could collectively negotiate with the rail authority.

City Attorney Gary Baum has already drafted a separate memorandum of understanding for the cities to sign, but the document has yet to be approved by the various legislative bodies along the Peninsula. (Palo Alto will vote on that memorandum Monday night.)

"I think the point we're trying to make to the HSRA (High Speed Rail Authority) is that they should not predetermine the outcome," Kishimoto said. "We expect that it will be a truly open process."

The city has also drafted a letter to Don Gage, chairman of Caltrain's board of directors, asking that the section specifying the four-track design be removed or altered.

"This level of specificity indicates that options and alternatives will be determined without meaningful public input and consultation," the letter reads.

The council will discuss three high-speed rail issues -- the Caltrain/Rail Authority memorandum, the Peninsula cities memorandum and the city's "scoping" letter to the rail authority outlining issues it wants included in an upcoming environmental-impact study -- at its meeting at 7 p.m. on Monday, March 30, at Council Chambers in City Hall, 250 Hamilton Ave.