City Comptroller Mark Levine launched an investigation Thursday into the Big Apple’s popular outdoor dining program — citing concerns that more than half of restaurant applicants are stuck in limbo.

Levine addressed a letter requesting records related to the program’s approval and review process to Department of Transportation Commissioner Mike Flynn and the Director of the Mayor’s Office of Contract Services Kim L. Yu.

“Regrettably, my office hears regularly about issues related to the permitting process, which is deeply concerning,” Levine wrote to the agency heads.

“Restaurants are struggling to cut the red tape on a slow and cumbersome permitting process,” he added.

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Levine noted that the DOT has submitted a mere 1,225 permit applications for the program — with over 62% of those not submitted until this year.

The Comptroller’s office also found a total of 2,390 eateries still waiting for approval as of January — a tiny fraction of the city’s estimated 25,000 restaurants.

“With summer approaching, DOT and MOCS must streamline and make more transparent their
review process and approve sidewalk and roadway cafés in time for the season,” Levine continued in the memo.

The Comptroller’s office registers the permits given out to restaurants — and since 2024 has allowed DOT to let agency-approved restaurants operate their outdoor dining spaces while waiting for official permits to speed up the process.

The Comptroller’s office is required to register the permits within 30 days of businesses receiving agency approval — and Levine noted concern that the MOCS and DOT do not have similar time limits.

Levine is requesting details and documents from the agencies that include step-by-step approval processes, the number of DOT staff working on the restaurant applications, and the actual timeframe for review per application.

A spokesperson for the Mayor’s Office did not immediately respond to The Post’s request for comment.