Mayor Bill de Blasio on Friday took the extraordinary step of pushing out his embattled investigations commissioner, Mark G. Peters, the culmination of a fierce rivalry between the two powerful men.

Mr. Peters was called to a meeting Friday afternoon with the first deputy mayor, Dean Fuleihan, and asked to resign, according to Eric F. Phillips, the mayor’s press secretary. Mr. Peters refused, and Mr. Fuleihan told him he was being fired.

No mayor has removed an investigations commissioner from office in recent memory; the position is understood to come with a large degree of independence that allows impartial scrutiny of all areas of government, including the executive branch.

But the relationship between Mr. Peters and the mayor had severely deteriorated over time, and the last straw for the mayor was an independent investigator’s report that found that Mr. Peters had abused his power and mistreated underlings, and said that he was “cavalier with the truth.”

Mr. de Blasio will name Margaret Garnett, the state’s executive deputy attorney general for criminal justice, to replace Mr. Peters. Her appointment must be approved by the City Council.

“Nothing matters more than integrity in public service,” Ms. Garnett said in a statement. “As commissioner for the Department of Investigation, I will make it my mission to ensure that everyone working for New York City adheres to the highest standard of ethics and is deserving of the public’s trust.”

Although the stakes and circumstances are different, Friday’s action recalled the recent firing of former Attorney General Jeff Sessions, who was asked to submit a letter of resignation.

Mr. Sessions had irked President Trump for recusing himself from the investigation into possible collusion of his presidential campaign with Russia. Mr. Peters had irked the mayor with his frequent investigations of government failings and errors.

The City Charter says the mayor has the power to remove the investigation commissioner, as long as he gives an accounting of his reasons for the firing and allows the commissioner “an opportunity of making a public explanation.”

The mayor prepared a written statement that cited the independent investigator’s conclusions, including that Mr. Peters had conducted himself “in a manner indicating a lack of concern for following the law,” had made “deliberately misleading statements” in testimony before the City Council, and had engaged in “intimidating and abusive behavior.”

It said Mr. Peters’s removal would take effect after three business days, a period that is apparently intended to allow time for Mr. Peters to make the public explanation mentioned in the City Charter.

Mr. Peters fell far and hard. A longtime friend and political associate of the mayor, he served as the treasurer for Mr. de Blasio’s 2013 mayoral campaign. When Mr. de Blasio, after taking office, appointed him as the commissioner of the Department of Investigation, the choice was greeted with skepticism, with critics asking whether someone so close to the mayor would be independent enough to pursue investigations into the administration.

Mr. Peters ultimately quieted those critics, issuing reports that touched on the city’s failures to properly inspect for lead paint contamination in apartments of the New York City Housing Authority, and the lifting of deed restrictions on a Lower East Side nursing home that allowed the facility to be sold to a luxury condominium developer.

The reports exposed embarrassing lapses at City Hall and agencies that report to the mayor, and Mr. de Blasio often took issue with the findings.

The mayor clearly chafed under Mr. Peters’s microscope, and had considered firing Mr. Peters seven months ago but decided against it; city officials seemed leery of the possible backlash over firing an investigator who had taken a critical look at the mayor’s governance.

But Mr. Peters finally overreached: Earlier this year, he staged a takeover of an independent office that conducts investigations of the school system. When the head of the office, Anastasia C. Coleman, resisted the takeover, Mr. Peters fired her.

She then filed a whistle-blower complaint, which led to the appointment of an independent investigator: James G. McGovern, a former federal prosecutor. The report gave the mayor the impetus and evidence to force Mr. Peters out.

The City Council was a strong ally of Mr. Peters in his clashes with the mayor’s office, especially under the current Council speaker, Corey Johnson. But the whistle-blower report greatly undermined that support, including the allegations that Mr. Peters misled the Council.

Mr. Johnson provided a statement on Friday that showed the extent to which that relationship had deteriorated. Mr. Johnson credited Mr. Peters for exposing “significant issues” at the housing authority and in other agencies, but said “the McGovern report raised questions about his ability to continue in his role.”

Mr. Johnson added that the Council would “engage in an advise and consent process,” an apparent reference to its role in approving a new commissioner.

But the chairman of the Council’s committee on oversight and investigations, Ritchie Torres, praised Mr. Peters for his independence, and characterized his firing as unprecedented, adding that he “strongly disagreed” with it.

Mr. de Blasio, in a statement released after the dismissal, thanked Mr. Peters for his service but saved his praise for Ms. Garnett.

“Margaret has spent decades protecting the public’s interest, prosecuting criminals both inside and outside of government,” he said. “She is fiercely dedicated to defending what’s right and will bring that independence and integrity to the Department of Investigation. I thank Mark Peters for his service and look forward to the City Council’s consideration of Ms. Garnett’s appointment.”

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