The state’s top education official still doesn’t see eye to eye with the de Blasio administration about the city’s plans to fix its struggling schools.

In her most direct criticism yet of the city’s plans, Board of Regents Chancellor Merryl Tisch said the city was wrong not to close any of its lowest-performing schools right away at a forum in Manhattan on Thursday.

“Having visited enough schools that are failing, I can say that my gut tells me it is a mistake,” Tisch said. “If you are not able to do a couple basic things when you are organizing your schools, you simply cannot create a new star out of a patchwork of clouds and rain and storm.”

Tisch’s comments are unsurprising, given her support of school closures in the past — a position she reiterated in a January letter to the governor’s office. But they are another sign of the uneasy accord between the state and the de Blasio administration, which has been pouring resources into its School Renewal turnaround program with the guiding philosophy that most schools can improve if teachers and school leaders are given the help they need.

The city is also required to submit annual improvement plans for its lowest-ranked schools to the State Education Department, which Tisch oversees. Schools are now beginning to draft those plans for next year.

Still, city officials haven’t taken school closures off the table themselves. If the schools don’t improve in the three-year timeline they set out in November 2014, the city will consider more dramatic changes, Mayor Bill de Blasio has said. Before that, the schools will receive intensive teacher training, funding increases, an extra hour of instruction, and summer learning opportunities for students, among other resources. (Only a subset of the city’s 94 Renewal schools saw those changes this year.)

As the first full school year under the de Blasio administration comes to a close, Tisch said that she will be paying special attention to staff changes at two long-struggling Brooklyn high schools, Automotive High School and Boys and Girls High School. Those two schools have been designated “out of time” to make changes, and all staff members will be required to reapply for their jobs as the school year ends.

Tisch said she remains skeptical of that rehiring process, which the city negotiated with the teachers union.  Hiring committees will be made up of representatives of the teachers union, principals union, and Department of Education.

“We are waiting for a final report of two of these schools that are perpetually failing now for some of them as much as 15, 16, 17 years,” Tisch said. The rehiring “will require enormous collaboration between Mr. Mulgrew’s shop and mayor’s office and Chancellor Farina’s office,” she added, referring to teachers union president Michael Mulgrew.

A spokeswoman for the education department declined to comment.

Tisch’s comments came during an hour-long appearance at a Crain’s Business breakfast. In her speech, the chancellor doubled down on a few policies she has spearheaded as the head of the Regents since 2009 — some of which have come under heavy fire recently. The decision to simultaneously introduce a teacher evaluation system tied to test scores and raise the proficiency bar on those tests during the 2012-13 school year, Tisch acknowledged, wasn’t perfect.

“When you change a broad system and displace people from comfort zones, you have to accept that error is a possibility,” Tisch said. “Not all charter schools will succeed. Not all tests will be perfect. Not all accountability measures will be error-free.”

Responding to questions from the moderators, NY1 education reporter Lindsey Christ and Crain’s assistant managing editor Erik Enquist, Tisch also offered a wholehearted endorsement of mayoral control as legislators continue to work out the future of city’s school-governance law, which expires in June.

She also addressed questions about the state education department’s recent decision to reject all 15 charter applications submitted in the most recent application round, saying she had grave concerns about the number of low-performing schools whose charters have been up for renewal over the last year. Tightening up the state’s new-school approval process, Tisch said, was one way to ensure that the sector is full of high-performers.

“We are trying to make sure that every charter that is given out by the state education department meets certain quality requirements so that we can be sure, to the best of our ability, that they can succeed,” Tisch said. “Do we really want to be in the business now of publishing a public list of failing charter schools?”