SafeTrack work is underway on the Red Line, below, as a Metrobus travels overhead at the NoMa-Gallaudet station. (J. Lawler Duggan/For The Washington Post)

Metro’s SafeTrack maintenance program will cost significantly more than anticipated and take at least three months longer to complete, according to a progress report released Wednesday.

The report by the Federal Transit Administration estimates that the total cost of the project will be $118.8 million — nearly twice the $60 million price tag Metro General Manager Paul J. Wiedefeld floated in June.

Only $80 million of the estimated cost results from the 15 targeted safety surges — $20 million is budgeted for SafeTrack work on nights and weekends outside of major surge areas and $20 million for estimated contingencies.

The Metro board budgeted $65 million for the project in its fiscal 2017 capital improvement budget. But since the start of the program, Wiedefeld has said repeatedly that costs could rise depending on the extent of the problems crews discover.

Additionally, the FTA report confirms what had already become apparent after recent changes to the SafeTrack schedule. Although the project was originally expected to conclude by March 2017, managers are now predicting a June 2017 completion date. The timeline could stretch even longer. The FTA report said the agency is expecting Metro to deliver another updated SafeTrack schedule next month.

Thomas Lipinsky, spokesman for Jack Evans, chairman of the Metro board, said the new numbers and the protracted timeline aren’t a surprise.

“The general manager said from the outset that the estimated $60 million cost of SafeTrack could fluctuate, and [D.C.] Council member Evans’s understanding is that the increase is due to both additional findings and improved ability to execute maintenance work,” Lipinsky said.

Even so, according to the report, Metro hasn’t determined how to pay for $41 million of the project costs. About $77 million is expected to come from federal grants.

The year-long maintenance program is focused on the 15 worst sections of track in the system, and the progress report offers a picture of the recurring problems plaguing the project as well as recent developments aimed at improving the quality and efficiency of repairs. The report was prepared by Hill International, a Philadelphia-based construction consulting firm.

According to the report, some of the progress on repairs has been hampered by a lack of coordination between departments at Metro as well as issues over how to balance scheduled maintenance work in targeted surge zones with the need to direct resources to urgent repairs in non-surge areas.

Also, the consultants said it has become clear that the 12-hours-a-day, six-days-a-week schedule for the SafeTrack repair crews has taken a toll on efficiency. “The issue is slowly being worked out,” consultants wrote, “but has had a negative effect on production.”

At the suggestion of the outside contractors, SafeTrack Director Laura Mason has hired a SafeTrack coordinator, William Baker, who is responsible for aiding communication across work crews and ensuring that items on a quality-control punch list are addressed before the end of each surge. Mason also hired a scheduler to manage an execution schedule and conduct daily progress calls as well as a business analyst to review cost data and find opportunities for savings.

Concerns about the quality of the repairs have been raised since the beginning of SafeTrack. This summer, FTA inspectors found multiple instances in which track problems were ignored, even after they had been highlighted on daily inspection sheets.

But the report released Wednesday indicates that Metro is trying to beef up its quality-control process. For example, starting with Surge 8, staff began conducting pre-surge inspections to tabulate all the defects in areas targeted for repairs. Additionally, officials have been compiling daily logs of conditions and problems on the tracks as well as a punch list at the end of each surge to indicate work that remained unfinished.

The Washington Metropolitan Area Transit Authority “is still developing the processes and procedures for post-surge work,” the report says.

Wiedefeld has defended these mid-project changes, acknowledging that repairs made in the initial surges were not perfect and adding that he and his staff have had to develop strategies on the fly to improve coordination between work crews and guarantee the quality of repairs.

“We pushed very hard to get this thing done very quickly,” Wiedefeld said at a SafeTrack news conference last month. “In a perfect world, you would study it for a year and come up with this. We didn’t have that luxury. So, basically, we had to jump into this thing. We’ve all learned along the way about how we can do this better.”

On Wednesday, the FTA also released daily reports of inspections conducted by Department of Transportation staff throughout September. Throughout Surges 8 and 9, inspectors delivered regular laundry lists of problems they spotted along the tracks. They found few serious safety problems and instead highlighted one-off issues spotted on the tracks — loose fasteners, deteriorated wooden rail ties and decrepit third-rail insulators. They indicated that most of those issues were fixed once inspectors pointed them out.

An inspector did note a safety lapse related to the position of roadway flagmen, whose job it is to stand on the end of either side of the work zone and watch for any trains that might accidentally pass signs indicating they must stop.

“During my observation I watched,” the flagmen “engaged themselves in conversation with the men in the work group . . . [They ] should have been positioned a minimum of 500 feet from the actual work zone,” inspector Terrell A. Williams wrote while watching work on the western end of the Orange Line.

That same day, Williams wrote, a flagman “could not be reached by the company radio” when another Metro employee tried to contact him. But he was able to be reached on his cellphone.