Weeks before the start of school, the state Education Department has issued an ultimatum to a charter school popular with Philadelphia-area families: Stop using physical facilities for face-to-face learning, or risk being shut down.

The order means that 500 children - roughly half the school - will likely be scrambling for new places to learn come September. The changes forced the school, Education Plus Academy, to lay off or slash hours for many of its staff, some of whom had just been hired or promoted.

Parents and the school's CEO say the abrupt move, which came on Tuesday, is further evidence that the Wolf administration is gunning for charter schools. That was the same day the governor asked a Delaware County court to dramatically curtail special-education and payments to charter schools in Chester City.

"Everybody knows the governor doesn't support charters," said Nicholas Torres, the school's CEO and one of its founders. "He specifically doesn't support cyber charters."

State officials denied that.

"That's totally untrue," said John Hanger, Wolf's secretary of policy and planning. "The governor has made the point that he supports good-performing charters and holds accountable those that are not performing."

Ed Plus, which opened in 2012, operates on a blended model. It is a cyber school aimed primarily at special-education students, but it also has offered face-to-face learning opportunities with teachers and other education staff at "learning centers" throughout the state, including six in Philadelphia and its suburbs.

Most students attended learning centers most days.

The crux of the state's argument is that Ed Plus and others ordered to shutter physical sites are running afoul of their charters: They were granted permission to operate as cyber schools, and stepped beyond those bounds. Officials said the school had been warned on multiple occasions.

"Cyber charter schools shall not represent or suggest to parents that their children will have the option to be present at its physical facility" for reasons other than tutoring, testing, and supplemental special-education services, a Department of Education official wrote to Torres Tuesday.

Jeff Sheridan, Wolf's spokesman, underscored the point.

"These can't be backdoor brick-and-mortar charter schools," Sheridan said.

Ed Plus is welcome to apply to operate as a brick-and-mortar charter school, Sheridan and Hanger emphasized.

The Education Department issued a statement Monday that there had been confusion and complaints across Pennsylvania about the use of cyber charter school facilities, and that its action was meant to clarify the law.

"Education Plus Academy Cyber Charter School is the only school we have heard from that is having issues complying with the laws and department guidelines governing cyber charter schools," the statement said.

Torres said that he was not violating his school's charter and that he had had conversations over the past several years with the state about Ed Plus' use of learning centers.

Amy Millar, a parent of three children set to start first, third, and fifth grades at Education Plus on Sept. 8, was blunt.

"It was a kill order," Millar said. "I feel like there's been a death in the family."

The school had supplemented the cyber curriculum with art, gym, and other activities, but those have all been cut because of the state's order.

"You can have 15 kids in a classroom setting working at different levels, and they're active, they're engaged, they're not frustrated," said Torres, who has extensive background in Philadelphia education circles. He is a former president of Congreso de Latinos Unidos, and founded Pan American Academy Charter, a brick-and-mortar school.

Millar said she grew frustrated with her home district - Abington - when her two older children, both of whom have special learning needs, were languishing in their public school.

Millar said her children had made significant gains at Ed Plus. Her daughter finished third grade at her public school barely reading at a kindergarten level, but is set to enter fifth grade reading at grade level now, she said. And Millar's son, who has autism and a tic disorder, used to try to flee school daily, she said.

He has never tried to escape at Ed Plus, Millar said. Instead of being upset to go there, she said, he is distraught when he can't go to school.

"And now, I'm in this spot where I have to call the school that failed my kids and reenroll them," said Millar. "I'm heartbroken over this."

To comply with the state's cease-and-desist order, Ed Plus is shutting learning centers in Chester, Clifton Heights, Abington, and Somerset immediately. It is also limiting the number of hours regular-education students can attend learning centers to three per day. Those students will only be able to receive tutoring, not instruction, as they had been.

Special-education students can use the centers from 8 a.m. to 3 p.m. Friday, but only for tutoring and supplemental services.

Ed Plus had also planned to expand to high school this year. It will not do so now, officials said.

Those changes mean that many families will be forced to go elsewhere.

Jo-Ann Rogan pulled her two sons from the Philadelphia School District in the face of budget cuts and frustration with services for her older son, who has special needs.

Her boys found a home at Ed Plus, she said, thriving academically, with project-based learning, and socially, with a good mix of regular- and special-education students.

"It's been amazing," said Rogan. "My kid has made huge progress, and he's been happy for the first time in school. The last two years have been healing and good for him."

She will likely keep her older son at Ed Plus for this year, but the new model will not cut it for her younger son, a regular education student.

"He's a really busy kid," Rogan said. "He needs to go to school."

Like Millar and many others, Rogan said she was poised to fight on behalf of Ed Plus.

Torres said the Ed Plus board will meet this week to discuss options, and might seek an injunction to bar the changes.

Cyber charter schools have come under fire for poor performance and little oversight, but Torres said the Ed Plus model is different.

"There's critique of cybers as a whole," he said, "but if cybers are to get better, they need this flexibility to engage with kids, face-to-face."