With the Metropolitan Transportation Authority preparing to phase out its iconic MetroCards at the end of the year, some riders are facing issues with the replacement system, One Metro New York — better known as OMNY — according to a new survey.

The Permanent Citizens Advisory Committee to the MTA found riders are generally positive about the transition on subways and buses — rating it 3.43 out of 5, on average. However, nearly 75% of the roughly 400 respondents had recently encountered at least one issue with OMNY, ranging from readers not accepting their tap to late or “extra” charges.

The advisory committee, which provides transit riders with a voice within the MTA, also called on the MTA to “better integrate” OMNY with the Long Island Rail Road and Metro-North, which use the separate TrainTime app.

Danny Pearlstein, spokesman for the Riders Alliance, a separate transit advocacy group, said he had heard riders complain about issues with OMNY not working.

“When we switched from a nickel to a token or from a token to the MetroCard, we didn’t see these issues before,” he said. “If there are still bugs to be worked out, then they have to be worked out before the final switch is made” to OMNY, he said.

But Jessie Lazarus, deputy chief of commercial ventures at the MTA, questioned the results of the new survey in an emailed statement.

“It’s hard to take seriously a tiny online push poll when twice a year for the last three years, we’ve asked over 70,000 riders how they feel and tap-and-go crushes MetroCard every time,” she said, referring to the MTA’s own customer satisfaction survey.

About 75% of all transit riders have switched to OMNY, according to the MTA.

The MTA began transitioning away from the 30-year-old MetroCard with the launch of OMNY in 2019. It plans to stop selling MetroCards on Dec. 31, but riders will still be able to use them for at least six months after that.

Cubic Transportation Systems, a defense and transportation contractor, is implementing the transition under contract with the MTA.

OMNY allows transit riders to pay for their subway or bus trip with a tap of OMNY’s card or their own digital wallets, debit cards or credit cards.

The new report found 54% of riders gave OMNY a rating of 4 or 5 out of 5.

But it also found that 42% of riders said they’d had problems with OMNY readers not accepting their tap and 30% received what they perceived to be “extra charges.” Respondents who interacted with OMNY’s customer service scored it 2.21 out of 5.

It noted that, unlike with MetroCards, OMNY users are not able to immediately see their remaining balance or if a free transfer or weekly fare cap was applied after paying a fare.

“Riders need to see this information directly on the screen to better trust the system,” it said.

OMNY is still not available on Nassau’s NICE Bus system, where more than 40% of riders use the MetroCard. Officials are aiming to implement the new fare system there by the end of the year, though some riders’ advocates have expressed skepticism about that timeline, Newsday previously reported.

A biannual 4% fare and toll hike is scheduled for this year, though this could be delayed until next year, the MTA has said.