Citing traffic concerns, the mayor of San Rafael is requesting the Sonoma-Marin Area Rail Transit system halt plans to extend trains to Larkspur until a new downtown transit center can be built — a project that is at least five years away.

The letter from Mayor Gary Phillips and City Manager Jim Schutz to SMART General Manager Farhad Mansourian raises issues about traffic impacts to downtown San Rafael if trains continue to Larkspur as planned.

“We understand fully the value of people coming to San Rafael on SMART, but it does not appear there will be many people going to Larkspur,” Phillips said Friday. “It would benefit a few riders, but to the detriment of many.”

The SMART plan has trains crossing busy Second and Third streets then going through the Bettini Transit Center, which sees 9,000 passengers a day, to get to Larkspur. Phillips fears trains crossing those streets will serve to back up traffic not only downtown, but on nearby Highway 101 off and on-ramps.

In addition, in order to accommodate trains passing through the transit center, bus stops will move to the perimeter of the facility, creating more traffic problems, the city believes. The San Rafael to Santa Rosa rail segment is scheduled to begin operation later this year.

In December 2015, SMART officials announced the agency was in line to receive funding to extend the commuter rail service to Larkspur, with construction starting as soon as this summer and service starting next year.

Now the city wants to 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.

“We don’t want to see the interim approach become permanent, that’s a concern,” Phillips said. “We are supportive of SMART going to Larkspur, but we support it being done once and in the right way.”

Mansourian said he is preparing a response to the letter, but said to halt the extension is the wrong approach.

“Basically San Rafael is saying we should postpone going to Larkspur,” he said. “But we are already going out for construction bids. People voted for it to go to Larkspur. People have been paying taxes for it.”

Also a concern is SMART potentially losing several million dollars of federal funding that could evaporate if work does not commence in a timely manner.

“Getting the federal funding for the extension was tough and it would be unconscionable to risk losing that very hard-to-get money,” wrote Cynthia Murray, president of the North Bay Leadership Council, in a letter to SMART on the issue. “Please move forward with due haste.

“NBLC is aware that there will be some impact on street traffic along the train’s railway as the train starts running its regular schedule,” she wrote. “Those impacts are mitigated by things like having train sets that fit within city blocks and synchronizing traffic lights. Traffic will also be reduced as commuters opt to take the train to work rather than drive.”

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

“We are in favor of SMART going to Larkspur as soon as possible, that’s why we worked with SMART and others to develop an interim route through the transit center,” said Denis Mulligan, general manager of the bridge district. “We recognize it is less than ideal, but it facilitates SMART going to Larkspur.”