The U.S. Department of Education notified state officials that charter schools must be assessed the same way as traditional schools.
The issue surfaced in September when the state's latest standardized test scores were released. For the first time, charter schools were treated as districts, not individual schools.
That made it easier for charters to reach a federal benchmark known as "adequate yearly progress," or AYP.
About 59 percent of charters made AYP under the new method. Only 37 percent of charters would have made AYP without it.
A letter from federal officials released Wednesday orders Pennsylvania to re-evaluate charter schools' AYP status using the old standard.