A Harlem church is suing the state in an attempt to overturn a law that bars religious organizations from running charter schools even if the schools don’t teach religion, a move likely to prompt new debate about the separation between church and state.

The Reverend Michel Faulkner of New Horizon Church Ministry said he wants to open a charter school in Harlem or Washington Heights that would be affiliated with his church, but would not have a religious component to the curriculum. If successful, Rev. Faulkner could change the face of new charter schools, allowing churches, synagogues, and mosques to operate them in New York.

Across the country, church leaders can and do run such schools, but most are run through separate nonprofits or management organizations, not the churches directly.

Rev. Faulkner could apply to open a charter school through a nonprofit organization separate from his church, but he said yesterday he’s not interested in that approach.

“I just feel like it’s not fair,” he said. “We, as a religious institution, can certainly uphold the values of separation between church and state.”

He said he was galvanized to file the suit after seeing an Arabic-language school, the Khalil Gibran International Academy, open in Brooklyn this fall. The public school was founded by a devout Muslim, but is not affiliated with Islam or any religious institution. Rev. Faulkner said he saw a connection between his would-be charter school and Khalil Gibran.

“If an Arabic school can start up, certainly New Horizon can start a charter school in order to promote great quality education,” he said.

A spokesman for Americans United for Separation of Church and State, Joseph Conn, said the suit sounded groundless.

“It seems unlikely to me that a church would want to run a school that is devoid of religious content,” he said. “The whole purpose of the church is to teach and spread religion.”

The executive director of Gotham Legal Foundation, Jay Golub, said Rev. Faulkner is a community leader and the best person in his neighborhood to run a charter school. Mr. Golub, who ran for public advocate in 2005, said his foundation filed the suit on behalf of the church in federal court this week. He called it a case of “pure religious discrimination.”

“The New York Charter Schools Act is nothing more than an attempt by the State to erect a barrier for those who express their religious beliefs from access to public resources,” the suit states.

The suit is challenging a portion of the New York Charter Schools Act of 1998, which says a charter will not be issued to a school that is run by a religious organization or a school where religious doctrine is taught. It is asking the federal court to deem unconstitutional a portion of the state constitution that bars from public dollars for education purposes from going to religious institutions.

The arguments of the suit link it to the debate surrounding school vouchers — publicly funded scholarships to private schools used in a growing number of states and cities. Many students use the vouchers to attend parochial schools. Critics of vouchers often endorse charter schools as a better alternative because they avoid sending public funds to religious institutions.

Charter schools with strong religious ties are often challenged. A charter school in Florida with a Hebrew theme, the Ben Gamla Charter School, has faced criticism from its local school board for using textbooks with some religious themes.

A charter school group run by an evangelical Christian minister, the National Heritage Academies, was the target of a lawsuit by the Michigan chapter of the ACLU. The group claimed that a charter school run by National Heritage, the Vanguard school, was holding prayer sessions in schools.

A senior fellow at the education policy think tank Education Sector, Steven Wilson, said the arrangements can be fine.

“The key is whether or not they are proselytizing,” he said. “I don’t see the reason why church leaders shouldn’t be permitted — so long as it’s open to all students regardless of faith, and so long as there’s no religious teaching.”

The chairman of the country’s largest charter school, Donald Hense, said the constitutional separation between church and state should keep religious leaders far away from charter schools.

“Religious groups are interested first about whatever philosophy they proselytize,” he said. “Public money should not be used to support that.” He said he does not let religious leaders play any role at all in his school, the Friendship Public Charter School in Washington, D.C.

The CEO of the New York City Center for Charter School Excellence, James Merriman, said he hasn’t seen many examples in which churches have come forward and said they are disappointed they couldn’t start a charter school.

He said he has seen instances in New York where members of a church parish have successfully sought a charter and opened a school outside of their church.

“It was their dream to have a school. A school that served not just the parishioners’ children, but that served anyone within the community,” he said.