The Philadelphia School Reform Commission has permitted a city charter school to ignore deadlines for overhauling its leadership even as a federal criminal probe of the school intensifies.

In August, the commission ordered New Media Technology Charter School in Northwest Philadelphia to replace its top administrator and board chairman by Sept. 1 and to install a new board by Oct. 15 as conditions for receiving a new, five-year operating charter.

Benjamin W. Rayer, the School District's top charter administrator, said he expected the changes within the next several months. The only issue is when.

He said the commission authorized his office to negotiate a new timetable because New Media has been making a good-faith effort to make the changes and wants to ensure an orderly transition at a school that has met federal academic benchmarks.

The commission in the past ordered two other city charter schools to replace their boards and chief executive officers as conditions for continuing to operate. New Media is the first school to balk.

Former staffers say Ina Walker, New Media's chief executive officer, has said she is determined to remain at the school she helped found. Some teachers and parents have testified at SRC meetings that Walker's presence is essential for the school's academic success.

But Rayer said that while the school had made most of the 23 required changes, the commission remains adamant that New Media must meet all the conditions, including replacing Walker.

The commission said the changes were needed to address allegations of financial mismanagement and conflicts of interest that surfaced when the school applied for a new operating charter.

"We think we are being aggressive but reasonable," Rayer said.

Because negotiations are continuing, Rayer said, he could not discuss the proposed new deadlines.

Michael Frattone, New Media's attorney, said he and the school declined to comment.

The charter continues to operate with 483 fifth through 12th graders on campuses in the city's Stenton and Germantown neighborhoods.

Federal authorities who are investigating the school's operations recently subpoenaed all New Media's financial records.

Federal agents delivered the subpoena Nov. 24 to Charter School Choice Inc., a Philadelphia firm that provides accounting services to New Media, seeking financial records for the school since it opened in 2004.

Attorney Thomas P. Hogan Jr., who represents Charter School Choice, said the firm was cooperating.

New Media is among at least six local charter schools whose finances are being investigated by federal authorities and by the district's inspector general, according to sources with knowledge of the probes.

John J. Pease, an assistant U.S. attorney who is chief of the government-fraud and health-care-fraud unit, has assumed responsibility for the federal charter investigations. He declined to comment on New Media.

But sources with knowledge of the criminal inquiry say federal investigators are examining allegations that funds from New Media were used to pay some expenses of Lotus Academy, a private school in West Oak Lane, and the Black Olive, a vegetarian restaurant and a related health-food store in Mount Airy. All have ties to Walker and Hugh C. Clark, another New Media founder.

New Media has been paying $180,000 per year to rent its middle school building from Lotus Academy. Until recently, Clark chaired the boards of both the charter school and Lotus Academy.

New Media rents its high school building from a limited partnership formed by Anthony Repice, a part-owner of Charter School Choice, and B. Robin Eglin, chief executive officer of OmniVest Management L.L.C., the company that renovated the building.

Clark stepped down from New Media's board this fall to meet one of the SRC's conditions. Carol Sandra Moore Wells, a New Media board member, has assumed the leadership role.

Wells, a federal magistrate, cofounded Lotus Academy, according to her biography on the U.S. District Court's Web site.

She did not return phone calls seeking comment.

Rayer said the district had been working with Wells to arrive at new deadlines.

"She has stepped into a new situation that is challenging and difficult," he said.

Former staff members who did not want to be identified said that little money was available for supplies and that some certified teachers had left since the school year began.

And despite repeated promises to parents and teachers that the school would provide more books, one former staffer said the only new books at New Media this fall came from Germantown Settlement Charter School, which the district closed in June.

Contact staff writer Martha Woodall at 215-854-2789 or at martha.woodall@phillynews.com.