Eva Moskowitz is going after the de Blasio administration again — this time over timely payments to her charter schools.

The Success Academy CEO published a letter on the charter network’s website chastising the de Blasio administration for late payments to two of its schools. The public rebuke is the latest in a string of fights Moskowitz has picked with the de Blasio administration and one that, while relatively low-stakes on its own, draws attention to the network as it ramps up a legislative fight to raise the state’s cap on charter schools.

In the letter, Moskowitz wrote that nearly $2 million was due to Success Academy Harlem 3 on May 1 and has not yet been paid, and a $1.3 million payment to Success Academy Harlem 5 came days late. The money is the $13,777 per-student allocation funneled from the state to the city’s education department to charter schools, and spokeswoman for Success Academy said delayed payments were rare.

“The lack of explanation or even the courtesy of a response from DOE staff is baffling,” Moskowitz wrote. “Is this deliberate negligence or just dysfunction?”

Department officials said it was neither. Spokeswoman Devora Kaye said that payments are forthcoming and the city is “meeting all necessary protocols,” adding that an invoice for Success Academy Harlem 3 was submitted the Monday after the Friday it was due in April.

The letter’s sharp tone is typical of Moskowitz, who has been Mayor Bill de Blasio’s most prominent critic on education policy. The strategy has worked well for Success Academy, most notably after de Blasio nixed plans for three of her schools to operate in public school buildings last year. Moskowitz’s protest campaign resulted in a deal for free private space worth more than $5 million last year and, at the state level, legislation forcing the city to pay other charter schools’ rent bills in the future.

Last December, the city agreed to co-locate 10 new Success schools in public space. And Moskowitz was confident enough to taunt the mayor at an event Monday night, where Capital New York reported that she joked about possibly taking “a victory lap around Central Park in a horse-drawn carriage,” which de Blasio promised to ban during his mayoral campaign.

“Perhaps we should have a cap on the district schools,” she said.

The letter also comes as the city’s charter schools’ finances are under increasing scrutiny, and as Success continues to bring in millions in private fundraising at flashy fundraising events. Comptroller Scott Stringer is currently auditing the Success network, and City Council education committee chair Daniel Dromm sent a letter to charter-school operators in February asking them to send in audit documents.

The letter serves as a vehicle for Moskowitz — who has said she would like to run for mayor — to portray herself as unwilling to compromise on efficiency. She has cultivated that image for years, stretching back to her time leading marathon meetings of the City Council’s education committee about union contracts.

“Our opponents, who are ceaseless in their quest to find fault in our operations, would like nothing more than for us to be delinquent in our own financial obligations,” Moskowitz wrote.