Delaying extension of the SMART train from San Rafael to Larkspur would be “irresponsible,” the rail agency’s top official said in a letter to the mayor of San Rafael.

Citing traffic concerns, Mayor Gary Phillips sent a letter last month requesting the Sonoma-Marin Area Rail Transit authority halt plans to extend trains to Larkspur until a new downtown San Rafael transit center could be built — a project that is at least five years away.

But in a response issued Tuesday, SMART General Manager Farhad Mansourian said work must continue.

“The extension is fully funded, planning work has already been completed and construction is set to begin this summer,” Mansourian wrote. “Any delay at this juncture would be irresponsible for several reasons.”

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He cited San Rafael’s own traffic analysis that shows minor delays for drivers when trains go through the downtown Bettini Transit Center en route to Larkspur, and that the city signed off on the plan along with other agencies. The city has no way to stop the Larkspur extension, according to SMART.

The SMART plan has trains crossing busy Second and Third streets and through the transit center, the hub for 9,000 passengers a day, to get to Larkspur. The city fears trains crossing those streets will serve to back up traffic not only downtown, but on nearby Highway 101 ramps.

In addition, to accommodate trains passing through the transit center, bus stops will move to the perimeter of the complex, creating more traffic problems, the city said.

But Mansourian warned that delaying the Larkspur extension jeopardizes $48 million in funding and could increase costs by $3 million to $5 million each year of delay, with no funding identified to pay for overruns. A delay would also force contractors familiar with the SMART work off the project, creating a learning curve for those who come on later, he wrote.

Phillips, who sits on the SMART board, could not be reached for comment on the response.

In its letter, he asked that SMART put the brakes on that plan and instead wait until a site for a new permanent transit center is found and funding available. A new transit center — which could more easily accommodate bus and train service — would cost between $32 million and $42 million, according to preliminary estimates. Funding has not been identified.

Rep. Jared Huffman, D-San Rafael, whose district includes Marin, also wrote a letter to SMART last week urging that it continue to Larkspur.

“I’m writing to convey my deep concern that any significant delay could put the federal funding for this important project at risk,” Huffman wrote in a letter dated Feb. 9. “There was intense competition for all of these funds, and securing such substantial amounts of federal funding — in a difficult fiscal and political climate — is a remarkable achievement for SMART and our North Bay community that should not be taken for granted.”

He also worried about how President Trump’s administration might view a delay.

“My concerns are underscored by the uncertainty presented by the new administration in Washington, and the reality that any federal funds that are unused or appear unneeded are a prime target to be redirected by Congress or the new administration,” Huffman wrote.

He offered to facilitate a meeting between the San Rafael, SMART and other agencies to address concerns.

The San Rafael-to-Santa Rosa rail segment is scheduled to begin operation this spring, with the Larkspur extension opening in summer 2018 if it stays on track.

The Golden Gate Bridge district owns the San Rafael transit center and is supportive of the temporary work to its facility to get SMART trains to its ferries in Larkspur, which travel to San Francisco. The bridge district would build the permanent transit center.