An announcement by the California High-Speed Rail Authority on Friday did not give a reason for Morales’ departure but quoted Gov.
Under Morales' leadership, the rail authority was able to secure legislative approval for additional state funding and fended off several legal challenges that could have caused grave damage. Construction on the first, 119-mile segment in the Central Valley began in late 2015.
But the project has fallen about seven years behind schedule, encountered growing Republican opposition and floundered in its efforts to secure private investment.
Morales was unable to solve problems with the acquisition of property — an issue that led the lead contractor to file a $50-million claim related to delays. Agreements with utilities, railroads and other entities affected by the bullet train's route also dragged on.
In December, the Federal Railroad Administration warned that the cost for building the 119 miles from Madera to Shafter could increase by 50%, to about $10 billion, because of all the problems. But Morales and rail board Chairman Dan Richard said that estimate was wrong.
Officials close to the rail project on Friday offered a variety of reasons Morales might be leaving.
Some suggested that anybody in the job would be exhausted after five years of struggling with political, legal and engineering challenges. Others said that while Morales — who was paid an annual salary of nearly $400,000 — had helped to keep the project alive politically, he mismanaged its operational aspects.
And an internal rail authority survey earlier this year obtained by The Times reported that employees complained morale was low and had declined in each of the last three years. Employees interviewed by The Times said turnover was high, leaving staff overworked.
Morales stepped into the job shortly after Brown signaled that he strongly backed the project and began installing his representatives on the rail authority board. The prior chief executive, Roelof van Ark, had been criticized for shunning the political necessities of the job and putting his focus on engineering. At the time, the authority was under pressure for having many vacant positions.
Before his appointment, Morales had been working on high-speed rail at Parsons Brinckerhoff, the state's main consultant on the project. His appointment drew criticism from Republicans and Democrats alike in the legislature, who worried about his relationship with the company affecting his management of the project.
Morales previously had worked as Caltrans director at the time when the controversial replacement for the earthquake-damaged eastern span of the San Francisco-Oakland Bay Bridge was under construction. He also served as executive director of the Chicago Transit Authority, on the Obama transition team and in former Vice President Al Gore's attempts to improve federal efficiency.
His departure from the California High-Speed Rail Authority comes six months after the project's chief deputy director, Dennis Trujillo, announced he would be leaving. That position remains open. Other top officials also have departed in recent months, including the chief administrative officer and the chief information officer for the project.
At the time Trujillo said he was leaving, rumors were swirling inside the rail authority that Morales would be going as well — something officials strongly denied.
On its website Friday, the rail authority announced a special board meeting to consider appointing a new chief executive would be held May 1, the earliest possible date that would comply with requirements for a 10-day notice. The scheduling indicates that the authority may have already begun searching for Morales' replacement.
Morales refused requests to comment on his departure. But in a letter to the governor, he cited a long list of his accomplishments:
"I am very proud of the progress we have made in advancing the nation's first high-speed rail system, against the odds and in spite of all the obstacles," Morales said. "We have 119 miles of construction underway through three major design-build contracts. To date, the project has supported thousands of jobs, put almost a thousand tradesmen and women to work, and injected upwards of $4 billion into California's economy."
7:15 p.m.: This article has been updated with additional details