The district said that the school has had poor academic performance for six years and failed to meet financial standards and audits.
It also accused the charter of improperly billing the district for about $770,000 for students who were not enrolled in 2012-13.
Walter D. Palmer, the school's founder, told the Daily News yesterday that the allegation of overbilling is misleading.
"Every year there is a reconciliation and an accounting of whether a charter school owes the district money or whether the district owes the school money," Palmer said.
For more than a year, he said, lawyers for the charter school have been talking with the district and agree that the school owes the district $500,000, not $770,000.
"We are working on paying that back," Palmer said.
He said that in a previous year's reconciliation, the district owed the school more than $1 million.
He claimed that the district is "retaliating" against the school because it has fought the district's efforts to "cap" or limit its enrollment to 675 students since 2010.
The school now has 1,300 students at two locations: kindergarten through fourth grade in Northern Liberties; and fifth through 12th grades on Harbison Avenue near Cheltenham, in Frankford.
"The state law says that a charter school's enrollment cannot be capped," Palmer said.
Palmer said that the school won a legal battle in Commonwealth Court, and that the district is appealing that ruling to the state Supreme Court.
"If we can enroll more students, then every other charter school in the city will try to expand," he said.
In a statement yesterday, Superintendent William Hite said: "This difficult decision was made with substantial evidence that this school is not serving the needs of students and their families.
"We require better student outcomes from a public institution that was granted a charter to educate children."
Palmer said his school has between 230 to 250 children who qualify for special-education programs, a higher percentage than other charters.
A woman leaving the school yesterday with her fourth-grade daughter, who uses a walker, called the Palmer school "a godsend."
Another parent, Christopher Sullivan, said he travels 45 minutes each way on the No. 15 trolley to bring his 5-year-old daughter Chrisette to the school from West Philadelphia.
"I think it's an excellent school," Sullivan said.
On Twitter: @ValerieRussDN