The commuter rail line between Airport Boulevard just south of Windsor and downtown San Rafael will cost $427.9 million to complete, about $25 million more than the previous estimate three years ago, officials said.

The increase in cost reflects a lengthening of the initial operating segment as Sonoma-Marin Area Rail Transit officials seek to eventually extend the line south to Larkspur and north to Cloverdale.

SMART general manager Farhad Mansourian on Wednesday presented the first estimate of the line's cost since the rail authority board decided in 2011 to build it in phases because of the recession.

In 2008, voters in the two counties passed a quarter-percent sales tax to fund the 70-mile Larkspur-Cloverdale line and an accompanying bike path.

The original estimate was $541 million, according to SMART's July 2008 financial plan. By 2011, the estimated cost had risen to $695 million. Wednesday's report put the project's total cost at $657 million.

When the economy tanked and sales tax revenues failed to meet expectations, the line was scaled back to 34 miles from downtown Santa Rosa to the Marin Civic Center at a cost of $403 million.

"In two years, we have come a long way and accomplished a lot," Mansourian said. "We have been very successful at pursuing other funds."

SMART so far has generated $125.3 million in sales tax revenue, $180 million from bond proceeds and $122.6 million in grant funds, according to the report.

The rail authority still faces a $230 million shortfall to extend the line north to Cloverdale and south to Larkspur and complete the bike path.

Mansourian said the agency expects to start train service in late 2016, two years later than originally predicted. The cars, which were developed in Japan, are being assembled in Illinois and should be delivered in spring 2015, he said.

Critics said Wednesday that the rail authority's report does not sufficiently plan for a future recession and does not identify funding for rail operations.