Nearly a month after The New York Times announced that the 2018 podcast “Caliphate” did not meet its journalistic standards, a public radio association has accused The Times of committing ethical lapses in its efforts to make amends.

The Public Radio Program Directors Association, which represents executives at public media outlets across the country, sent a letter of complaint on Monday to The Times’s audio division. It was signed by executives at 26 public radio stations that carry The Daily, the popular Times podcast hosted by Michael Barbaro.

In mid-December, an Editors’ Note in The Times laid out the journalistic problems in “Caliphate,” a 12-part series that sought to shed light on the Islamic State. In the note, The Times said it had given too much credence to the false or exaggerated account of one of the podcast’s main subjects, Shehroze Chaudhry, a Canadian who claimed to have taken part in Islamic State atrocities. On the day the note was published, Dean Baquet, the executive editor of The Times, gave an apologetic audio interview to Mr. Barbaro that was attached to “Caliphate” as a 13th installment. Mr. Baquet described the problems as “an institutional failing,” saying the podcast’s errors should not be blamed on “any one reporter.”

In its letter, the public radio association questioned why The Times did not disclose, as part of the audio interview with Mr. Baquet, that Mr. Barbaro was in a romantic relationship with Lisa Tobin, an executive producer of “Caliphate.” The letter also criticized Mr. Barbaro for sending messages to reporters, including journalists at NPR, that tried to influence their coverage of The Times’s handling of the erroneous reporting in “Caliphate.”

“We feel Barbaro’s actions are in direct conflict with our ethical guidelines and they call his general credibility into question,” the letter said.

The letter also took issue with The Times’s personnel decisions concerning the co-hosts of “Caliphate,” the investigative reporter Rukmini Callimachi and the audio journalist Andy Mills.

After the correction, Mr. Baquet said Ms. Callimachi had been removed from covering terrorism and international conflicts, a prestigious beat in which she had won a number of journalism awards over more than a decade.

Shortly after the Editors’ Note was published, Mr. Mills served as the guest host of an episode of The Daily. The letter said the decision to reassign Ms. Callimachi “while giving greater visibility to her white male counterpart” suggested that The Times was not doing enough to guarantee equal treatment of its employees.

The letter continued, “We respectfully request that The New York Times acknowledges and takes responsibility for these lapses in judgment and takes steps to remedy them now and in the future.” Among those who signed the letter were program directors and station managers at public radio stations in Chicago, Los Angeles, San Francisco, Seattle and Washington.

Mr. Barbaro and Mr. Mills declined to comment. Sam Dolnick, an assistant managing editor of The Times who oversees the audio team, replied to the association on Tuesday in a letter made available by a Times spokeswoman.

Mr. Dolnick wrote that Mr. Barbaro “deeply regrets” having sent private messages to journalists who covered the “Caliphate” correction, adding that Times editors “have discussed their expectations with him going forward.”

Mr. Dolnick defended The Times’s decision not to disclose Mr. Barbaro’s relationship with Ms. Tobin as part of the interview with Mr. Baquet. “This was an audio version of our Editors’ Note, not an accountability interview, which Dean had already given to NPR,” Mr. Dolnick wrote. “With that understanding, we did not see a need to make reference to Michael’s relationship with Lisa Tobin.”

Mr. Dolnick expressed regret over Mr. Mills’s stint as a Daily guest host. “The timing of that episode was a mistake and sent an unintended signal that undermined the gravity of the ‘Caliphate’ Editors’ Note,” he wrote.

In the weeks since the “Caliphate” correction, people who worked with Mr. Mills before he joined The Times in 2016 have made complaints on social media about his behavior toward women in the workplace and in social settings.

Accounts of his conduct were described in a 2018 article in New York Magazine’s The Cut about workplace problems at the New York public radio station WNYC, where Mr. Mills previously worked. He has also been a focus of recent articles in The Washington Post and NPR.

Radiolab, the WNYC podcast where Mr. Mills worked before joining The Times, issued a statement on Jan. 7 to address the recent complaints. “We hate that this happened and we apologize to those we failed,” Radiolab said in the statement. “At the time, show leadership initiated a response from WNYC to address Andy’s behavior, but it didn’t happen fast enough and it didn’t do enough.”

The public radio association’s letter described Mr. Mills as “someone with a history in public radio.” In his reply, Mr. Dolnick wrote, “You also referenced allegations of Andy Mills’ misconduct, which we take very seriously. We thoroughly review all complaints received, and will take any appropriate corrective action.”

Abby Goldstein, the president and executive director of the Public Radio Program Directors Association, said she wrote the letter after station executives had contacted her with concerns. The complaints involving The Daily, which is carried by roughly 200 public radio stations nationwide, had come more from people working in public radio than from listeners, she added.

“Where the feedback is coming from in most cases is within our own industry — staff, board, donors,” Ms. Goldstein said. “Staff more than anything. Stations feel we have a big responsibility to staff.”

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