The 43-mile 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.

Sonoma-Marin Area Rail Transit officials hope to eventually extend the line even farther, to Larkspur on the south and Cloverdale on the north.

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-cent sales tax to fund the entire project -- a 70-mile Larkspur-Cloverdale line and an accompanying bike path.

The original estimate for the full project 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 collected $125.3 million in sales-tax revenue, $180 million from bond proceeds and $122.6 million in grant funds, according to the report. The total revenue matches the cost of building the main segment from San Rafael to Airport Boulevard.

The rail authority still faces a $230 million shortfall to finish the rail line's extensions -- 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 train 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 possible future recession and does not identify funding for rail operations.

"The significant financial exposure of SMART is they don't have sufficient funds under any scenario to operate trains they've touted, because of future recession impacts on sales-tax revenues," said Mike Arnold, a Novato economist. "When the next recession occurs, they will have little choice but cut service and raise fares. They are putting their heads in the financial sand, not asking any hard financial questions for fear their analyses would generate answers they don't want to hear."

As the economy has improved, revenues have increased, said Erin McGrath, SMART's chief financial officer. This has allowed the agency to pursue additional grant funding to extend the first phase of the line by nearly nine miles, to a total of 43.

McGrath said SMART has set aside $15-$18 million per year for operations. "We have enough money to run the trains," she said. "We will run the trains."

SMART board members expressed pleasure with the project update.

"I remember when we were trying to scrape pennies together to afford this thing," said Mill Valley mayor Stephanie Moulton-Peters. "I'm happy to see there is additional revenue to build it."

Mansourian said that construction crews this year will be working to rehabilitate the rail line north of Guerneville Road in Santa Rosa and south of Petaluma. On Tuesday, workers began building part of the pathway between Bellevue Avenue and Hearn Avenue in Santa Rosa.

Jim Eddie, who represents the Golden Gate Transportation District on the SMART board, said the pieces of the project are starting to fall into place.

"It's not long ago we can remember the problems we had," he said. "We've moved through this. It's like a puzzle that goes together. We've done really well since the days we started."

You can reach Staff Writer Matt Brown at 521-5206 or matt.brown@pressdemocrat.com.