State Education Department spokesman Tim Eller said the change was made to bring calculations for charters into line with those of districts. Some charters have a wide range of grades and, like districts, would get a fairer evaluation that way, he said.
Many public school advocates said the change was part of continuing Corbett administration favoritism for charters and other school-choice options.
"It unfairly makes charters look better than they are," said Lawrence Feinberg, a Haverford School District board member and cochair of the Keystone State Education Coalition, a public school advocacy group.
In late July, without public notice, the state Department of Education filed the proposed change with the federal Education Department.
The change had not been approved by the federal agency by September, when the state announced test scores and AYP results using the new method for charters. Weeks later, the Pennsylvania School Boards Association said it learned of the change when reviewing test results.
Eller said last week that the proposal is a "routine amendment."
But in an e-mail last week, a U.S. Education Department official said: "The [Pennsylvania Department of Education] does not have the authority to apply this methodology . . . until the federal department has had an opportunity to review and approve its expanded application." The official said the federal department was still reviewing the request.
Eller said that while he was "not contesting their authority . . . we don't anticipate our request being rejected."
Under the new rules, charters did about as well statewide this year as public schools, and much better than regular schools in several urban districts.
About 49 percent of charters statewide made Adequate Yearly Progress in 2012, compared with 51 percent of all Pennsylvania schools.
In Philadelphia, about 54 percent of charters made the grade, compared with only 13 percent of public schools.
The school boards association said that if the old rules had been used, dozens fewer charter schools would have made AYP and charters would have performed much worse on average statewide than regular public schools.
Under the old rules, the association estimated, statewide, only 33 of 156 charters with PSSA scores - 21 percent - would have gotten the "Made AYP" designation, instead of 49 percent. In Philadelphia, association figures showed, 20 percent of charters would have made AYP, instead of 54 percent.
State Education Department AYP figures showed more charters making the mark than the association estimate. No figures for Philadelphia charters were provided.
Contact Dan Hardy at 601-313-8134 or firstname.lastname@example.org, or follow on Twitter @DanInq.