When the Regents adopted the new standards in 1996, it exempted nonpublic schools, with the understanding that the issue would be discussed later.
Under state law, school districts must transport pupils to nonpublic schools within a 15-mile radius.
A sponsor of the study and a teachers' union said the improvements resulted from smaller class sizes in the nonpublic schools.
By Pennsylvania law, this program is open to students, residing in the district who are home schooled or attend nonpublic schools.
Many nonpublic schools without a religious identity or affiliation are private schools designed to prepare students for college.
But hard evidence comparing the performance of public and nonpublic schools has proved elusive.
Most charities, churches, nonprofit organizations and nonpublic schools would shut down without volunteers.
She said the result could be bitter conflicts between the public and nonpublic schools.
Public and nonpublic schools have typically been wary of one another.
"Maybe we should have regulations for any nonpublic school that participates," he said.