Just months before Metro’s new Silver Line is scheduled to open, the agency building the rail line received more troubling news Wednesday about the project, which already is late and over budget.

The head of the project is resigning, and the agency’s board acknowledged that attempts to fix a key component of the new line have failed. Officials said they will use a work-around until a nearly $2 million permanent fix can be completed.

Wednesday’s news comes as the $5.6 billion extension to the Metro system already is seven months late and $150 million over its targeted cost. As of Wednesday, officials with the Metropolitan Washington Airports Authority still could not say when the project will be complete.

The resignation of Pat Nowakowski, executive director of the rail project, underscores concerns among those already worried about the MWAA’s management of the project.

Terry Maynard, a member of the Reston 2020 Committee, a neighborhood group that has been instrumental in pushing the project, said Nowakowski’s resignation exacerbates problems tied to the construction of the rail extension including the installation of radios that don’t meet code, leaky roofs at rail stations and technical problems with equipment and other issues.

Pat Nowakowski (Courtesy of MWAA)

“There have been too many surprises,” Maynard said. He said many parts of the project, such as the completion of power stations — an earlier issue in building the line — “weren’t closely inspected” when they were done. These things “should have been ironed out along the way.”

MWAA officials said Nowakowski’s departure is voluntary and is not related to the Silver Line problems. But the announcement comes at a critical time for the project, which is in the middle of a 15-day review period to determine whether the contractor, Dulles Transit Partners, has completed work necessary for the rail line to be turned over to Metro.

The Silver Line is the first extension of the 38-year-old Metro system in more than two decades and one of the largest infrastructure projects being built in the United States. Area leaders see the line as key to the region’s continued economic growth. This first phase of the project will have five stops, four in Tysons Corner and one in Reston at Wiehle Avenue. Preliminary work on the second phase, which will have six stops, including one at Dulles International Airport, has recently begun.

Meanwhile, Metro announced Wednesday that the agency’s chief financial officer, Carol D. Kissal, was resigning. Her resignation follows a federal audit that was sharply critical of Metro’s handling of billions of dollars in federal grant money. As a result, the Federal Transit Administration has restricted Metro’s ability to draw from federal grant funds.

Metro and the MWAA play key roles in the Silver Line. The MWAA is responsible for overseeing construction of the $5.6 billion rail line. Once construction is complete, Metro will operate the line. The addition is the first one constructed by an outside entity, and some say the fact that Metro did not build the extension itself complicated an already complex undertaking.

The $1.8 million contract the MWAA awarded Wednesday is to fix problems with a component that enables Metro’s central control center to communicate with train control equipment along the rail line. It was a no-bid contract because only one company makes the component.

Both agencies have drawn federal scrutiny for internal management practices and for the handling of contracting and procurement on large projects. In January, the MWAA was the subject of an inspector general’s report critical of its handling of $975 million in federal funds tied to the Silver Line project.

More recently, Metro was criticized for its management of billions in federal grant funds. In a 50-page draft report, the Federal Transit Administration said Metro awarded millions of dollars in no-bid contracts — including a $14 million no-bid contract to one vendor — skirted contracting rules and appeared to steer work to a preferred vendor that lacked the proper expertise.

Some observers are worried that the latest news will further delay the project. “It is not good for the top guy to be leaving,” Benjamin Ross, a transit advocate, said of Nowakowski’s departure.

He worries that the MWAA may have trouble quickly finding someone to replace Nowakowski. So few large transit lines are being built around the country that the “talent pool and experience pool are thin.”

But MWAA President and Chief Executive Jack Potter said the project will continue to move forward. “Pat’s departure leaves big shoes to fill, but we have an excellent staff that Pat has trained and our new vice president for construction, Ginger Evans, will be taking on a larger role as we search for Pat’s successor.” He said the authority will conduct a nationwide search for a replacement.

Nowakowski, who joined the rail project in 2009, would not elaborate on his new job. He said that he was recruited for the position and that the change had been in the works for a while. His last day on the job will be May 2. His yearly salary was $257,695.

“It’s bittersweet,” Nowakowski said of leaving the rail project.

In a memo to employees, Metro General Manager Richard Sarles said Kissal was resigning to take a “position in the private sector.” And Kissal, in an e-mail, said her departure was not tied to the FTA audit. “This opportunity for me has been in the works for several months.”

At Metro, Kissal oversaw the agency’s nearly $3 billion annual budget and was responsible for collection of revenue, buying parts and services, information and technology work and planning and development. She came to Metro in 2008, having previously worked at the District Department of Transportation as a deputy director and as treasurer at Amtrak, where Sarles and several of his top executives now at Metro also worked. As Metro’s CFO, she was paid $243,600 in 2013.

Sarles promised to make fixes and meet deadlines set by federal auditors to address problems.

In the memo announcing Kissal’s resignation, Sarles credited her with helping to create “financial stability” at the transit agency. He said she “led an overhaul and upgrade of Metro’s financial operations for improved management and oversight.”

“Carol’s been there for more than five years, and that’s pretty long service in what was a pretty difficult place when she came on board,” said Mort Downey, the first vice chairman on Metro’s board, who also serves as a federal government representative.

Kissal will be replaced by Blair Fishburn, Metro’s deputy chief financial officer. He will start Friday as Metro’s acting CFO, Sarles said in the memo.

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