A towering stretch of the F and G subway lines in Brooklyn that recently underwent a $275 million renovation needs more work, THE CITY has learned.

The Culver Viaduct — a steel-and-concrete structure that spans the Gowanus Canal — is plagued by “unsatisfactory drainage, leaking expansion joints and premature deterioration of structural braces” only three years after being rebuilt, according to MTA records.

The transit agency has set aside $666,000 in its current five-year Capital Program for a design study on how to fix the lingering issues of the 87.5-foot-tall structure, which includes the Smith-Ninth Streets and Fourth Avenue stations.

The project is “under development,” the records say, so construction costs will be addressed in a future budget. It’s listed on the agency’s online Capital Program Dashboard as a “wrap-up” to the viaduct work completed in 2016.

“They should have gotten it right the first time they did the work,” said Ivan Santiago, 63, who took an F train to Smith-Ninth Streets on Monday. “And it’s lousy that they have to do more work so soon.”

Reconstruction of the mile-long Culver Viaduct dates back close to a decade, as crews replaced the four tracks on top of the structure, waterproofed its concrete decks and installed new track drains. The project, in part, was supposed to combat deterioration to the 86-year-old viaduct’s crumbling concrete casing, whose underside was partially wrapped in protective netting.

Commuter Headaches

The work created a series of commuting obstacles for F and G train riders, who couldn’t use the Smith-Ninth Streets station for close to two years, and dealt with various skipped stops.

“It was a big inconvenience, a headache,” said Vanessa Escobar, 35, of Red Hook. “Sometimes, I had to spend more money to take a cab or I had to take a long bus ride to get to where I was going.”

The project also extended the G line’s Brooklyn terminal to Church Avenue and renovated the arch that runs across Fourth Avenue at the Fourth Avenue-Ninth Street station.

“Why did they do all that work if they have to come back and do more?” said Angel Hernandez, 48. “That’s a waste of money right there — it’s ludicrous.”

MTA officials noted the complexity of the viaduct project involving Smith–Ninth Streets, the tallest elevated station in the world. They don’t expect any upcoming work to require closure of the station.

“We need to achieve some fairly standard state-of-good-repair and maintenance goals on an extremely non-standard, unique structure that has required work to happen in phases,” said Shams Tarek, an MTA spokesperson. “We will hold ourselves and our contractors to the absolute highest standards of customer service, quality of construction, and safety, and look forward to renewing this structure for years to come.”

Meanwhile, an audit released Monday by State Comptroller Thomas DiNapoli flagged the MTA for repeated cost overruns and delays on capital projects, though the report did not include the work on the Culver Viaduct.

Transit watchdog Ben Kabak said the remaining structural work along the Culver Viaduct points to the MTA’s “inability to deliver quality work on time.”

“What a joke,” said Kabak, who writes the 2nd Ave. Sagas transit blog.

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