The Panel for Educational Policy rejected a plan to allow a Success Academy charter school to open inside a Brooklyn middle school Wednesday night, a move that could set up a new fight between the city and Success CEO Eva Moskowitz.

The city’s proposal would have allowed Success to open an elementary school in the building occupied by Andries Hudde Middle School in Midwood. Moskowitz said months ago that she postponed opening new schools in fall 2015 because the de Blasio administration assured the network that it would find public space for 10 of its new or expanding schools, which included Midwood.

But on Wednesday, the proposal won only six of the seven votes needed for approval. The rejection was panel’s latest display of independence from the de Blasio administration, which appoints eight of the body’s 13 members but has publicly encouraged panel members to speak their minds. (Only 11 panel members were present Wednesday, and it was not immediately clear whether one had abstained from voting on the Midwood proposal.)

“The mayor has asked that we make informed decisions. Informed decisions,” mayoral appointee Elzora Cleveland said before the vote. “We are not puppets to anyone. We do our homework to make these decisions. We really work hard. And we are not here to play politics.”

The vote comes as the de Blasio administration continues to push lawmakers to renew mayoral control of the city’s schools with just a few days left in the legislative session. Last month, Moskowitz wrote an open letter to the mayor questioning his management after the panel delayed a vote on the Success Academy Midwood proposal, which was first discussed at the panel’s May meeting.

“During your campaign, you claimed that you would be able to establish a better dialogue concerning the placement of charter schools,” Moskowitz wrote. “That is well and fine, but sometimes doing the right thing means standing up to loud voices and special interests that are just wrong.”

Panel members saw it differently. A few said they continued to be disturbed by the reputation Success Academy schools have for being bad neighbors and for the network’s policy of not filling seats that open up in its schools’ older grades. They also were concerned about limiting Hudde’s growth.

“I know the head of Success Academy explained a few months ago that it’s not fair to take in older kids who are way behind,” panel member Laura Zingmond said, referring to the network’s backfilling policy. Their model of not taking students in older grades “really bothers me,” she added.

The co-location would not have brought the Hudde building to its full capacity, according to the city’s estimates. The Bloomberg administration had also proposed co-locating a charter school with Hudde in 2013, which the city says only requires 57 percent of its current space. The middle school is also not a part of the city’s “Renewal” turnaround program, a factor that has concerned panel members in the past.

“The school is severely underutilized. And we know it,” Isaac Carmignani, a mayoral appointee who voted in favor of the proposal, explained after the meeting. “So what do we do? Just let it sit there?”

With more than a year before the Success school was scheduled to open, the city has time to propose alternate sites, though Moskowitz has said the city committed to moving more quickly. Department spokeswoman Devora Kaye said in a statement that the city was “committed to adhering to the state’s space law and to siting this school and will work with the panel, school communities and families to ensure we address their concerns.”

Success Academy representatives did not immediately respond to a request for comment.

The rejection was the panel’s second under de Blasio. It voted down the expansion and co-location for part of DREAM Charter School in May 2014, but approved a co-location for those grades in June.

The panel did approve three other proposals on Wednesday, two of which involved Success Academy schools. Success Academy Cobble Hill and Success Academy Williamsburg both received the panel’s approval to add a fifth grade to their buildings in 2016. Icahn Charter School 7 also won approval to add a sixth grade in 2016 after that proposal was delayed in May.