Head of California high-speed rail project calls it quits

Anthony Garcia and fellow workers on an elevated section of tracks of the California high-speed rail system in Fresno, Ca., as seen on Wednesday Feb. 1, 2017. Anthony Garcia and fellow workers on an elevated section of tracks of the California high-speed rail system in Fresno, Ca., as seen on Wednesday Feb. 1, 2017. Photo: Michael Macor, The Chronicle Buy photo Photo: Michael Macor, The Chronicle Image 1 of / 42 Caption Close Head of California high-speed rail project calls it quits 1 / 42 Back to Gallery

The head of California’s $64 billion high-speed rail project said Friday that he’s stepping down after five years pushing forward a vision of 220-mph trains that still faces stiff resistance from lawmakers and the public.

Jeff Morales, 57, told The Chronicle that uncertainty over the project’s future had nothing to do with his resignation, only a genuine desire to move aside after breaking ground on the nation’s largest infrastructure project.

“We’ve made a tremendous amount of progress, from being at a standstill to having $3 billion-plus of construction under way,” he said. “Frankly, I didn’t think I’d be here for five years. I had no gray hair when I started the job. I have lots of it now.”

Morales, who sent his resignation letter to Gov. Jerry Brown on Friday, plans to remain chief executive officer of the California High Speed Rail Authority through June 2, long enough for his replacement to be found. The search for a successor has begun.

Plans for a 500-mile rail line, with trains running between San Francisco and Los Angeles in two hours and 40 minutes, were launched in 2008 with a voter-approved ballot measure.

In May 2012, Morales was hired by the rail authority’s board as the project struggled to get off the ground, with agency staffing stalled, lawsuits looming over rights-of-way, and the Legislature yet to commit to construction.

Since then, the agency has bought more than 1,000 parcels of land and hired a handful of contractors to begin building 119 miles of rail line between Madera and Bakersfield.

But even as the workers build the line in the Central Valley, the project remains at least three years behind schedule, and a lack of funding threatens future progress.

As the public has grown increasingly skeptical, Republicans in Congress have asked the Trump administration to withhold funding. In February, the Federal Transit Administration responded by suspending $647 million for electrification of Caltrain, a move that will be necessary in order for high-speed trains to make the final leg of their journey to San Francisco.

Meanwhile, in Sacramento, the state’s cap-and-trade program, which essentially sells pollution credits to industry to fund projects like high-speed rail, has failed to meet revenue expectations.

Morales, who is known as a steadfast negotiator not afraid of the political fray, said he wasn’t deterred.

“Any big project, whether in California or elsewhere, goes through ups and downs,” he said. “We’ve been declared dead a number of times, yet we have a thousand construction workers on the ground. The fact is that this thing is going forward.”

On Thursday, the project succeeded in winning $1.25 billion through the sale of state bonds. The rail authority said it had spent or secured more than $20 billion to date and hopes to begin running limited train service between Bakersfield and the Bay Area in 2025.

Before heading up the rail authority, Morales ran the state Department of Transportation for 3½ years under Gov. Gray Davis. After that, he worked as a senior vice president at Parsons Brinckerhoff, an international transportation firm that has been a primary contractor for the rail authority.

In a statement issued by the rail authority, the governor applauded Morales’ work.

“Jeff was instrumental at a crucial point in time and led California’s high-speed rail project through a very challenging period,” Brown said. “His dedicated and skillful leadership is exactly what was needed.”

Morales said he plans to stay with the agency after June 2 as an adviser for as long as it takes to get his successor up to speed.

Kurtis Alexander is a San Francisco Chronicle staff writer. Email: kalexander@sfchronicle.com Twitter: @kurtisalexander