But proponents of the method like the Smiths and Applied Scholastics, the organization founded in 1972 to make Study Tech broadly available, say it's an effective, nonreligious teaching technique.
"Study Technology is a secular methodology intended to help students better understand what is being studied and apply it to real life," Pinkett-Smith wrote in an e-mail to ABCNews.com forwarded through her publicist. "NVLA integrates this methodology as a tool in instructional design by providing teachers the framework to design lessons and curriculum."
In a March interview with National Public Radio, Pinkett-Smith spoke about the school's alleged religious ties.
"I definitely want to make it very clear to everybody that the educational institution that we have, the school that Will and I have, is not a Scientology school ... it is not a desire of ours to educate children with Scientology, that is not what Will and I want to do. And our school is not, and I repeat, not a Scientology school."
The most ardent critic of Study Technology says he doesn't buy all the denials. Dave S. Touretzky, a professor of computer science at Carnegie Mellon University, created a Web site that dissects Study Tech and asserts that it is the Scientology religion disguised as education.
Touretzky said he became focused on Scientology after the group threatened to sue Carnegie Mellon and himself after he posted a secret document revealing what he called the organization's "creation myth."
"I can't say it [the school] is a Scientology church," he told ABCNews.com. "What they seem to have is some sort of a hybrid. Scientology repackaged for the Hollywood crowd. It's hitting all the politically correct elements ... but snuck in there is this Scientology stuff."
A spokeswoman for the Church of Scientology, Karin Pouw, would not comment on whether there was a relationship between Scientology and the NVLA. She referred all questions back to the school.
Other educators worry less about Study Technology's ties to Scientology and more about its overall effectiveness.
"I look at the Study Tech ideas and it doesn't seem sound educationally," said Jim McManus, executive director of the California Association of Independent Schools. He spent 14 years as an education consultant for independent schools around the country and says he has no personal animosity toward Scientology.
Dan Willingham, a psychology professor at the University of Virginia who has a background as a cognitive scientist and wrote the book "Why Don't Students Like School," has similar doubts about Study Technology's merits and says it is based on flawed theories.
"It's perfectly possible that the methodology is based on ridiculous principles and that something effective is happening in the classroom, but ridiculous principles certainly lowers that possibility," Willingham said.
Located in the city of Calabasas, just outside of Los Angeles, the New Village Leadership Academy is nestled alongside a main road and surrounded by palm trees and housing developments.
The NVLA opened its doors Sept. 3, 2008, after the Smiths paid nearly $1 million to lease the Indian Hills High School campus in the Las Virgines Unified School District for three years.