The ACLU lawsuit against the Tarek ibn Ziyad Academy claims the charter school runs roughshod over the line that separates church and state.
TiZA, as the school is known, serves mostly immigrant children, many of them from Muslim countries in Africa, Asia and the Middle East. And it makes no apologies for catering to Muslims.
Click here to view a PDF of the complaint.
Arabic language classes are offered and school leaders note how important parents find it to have time set aside for Muslim prayer - and that time is optional.
But the ACLU claims that lost classroom time is never made up. The federal lawsuit also questions the relationship between the academy and its charter school sponsor, California-based Islamic Relief USA.
It claims a prayer is illegally posted at the school's entrance and it questions the school's dress code, which prohibits girls from wearing short sleeves per Muslim clothing rules. And the suit notes that school buses don't pick up kids until an hour after class ends, with the gap being filled with a Muslim studies program that most kids are enrolled in.
"This is in many respects - almost all respects - a religious school, like a private religious school, except for one key thing: There's state money going in there," according to Chuck Samuelson, the ACLU's executive director.
There would be no lawsuit if TiZA were private, he says. But TiZA gets tax money, $3.8 million this year, which changes the ballgame.
"If they want to be a private school, then that's fine. But then they have to give up state money and if they want the state money, then they have to behave as a public school does."
The lawsuit also asks the school to give back a pro-rated refund to the state.
But the claims of illegal religious endorsement don't fly with Joe Nathan. He's a charter school advocate who runs the Center for School Choice at the University of Minnesota.
His own Jewish upbringing makes him especially sensitive to the idea of a school forcing one religion on students, Nathan says. But that's not what he saw when he visited the school.
"This is a school that is quite clearly not promoting one particular religion in its curriculum, in its assignments and in the materials that are used," he says. "I have seen religious materials used to promote one religion or another, in math or history or science, and so on, and I've found quite the opposite. In fact, what I've found was a real promotion of inclusion and tolerance and acceptance."
School officials were not available for an interview today. But the school did release a written statement saying it's surprised by the lawsuit, which it says is "without merit."
The fact that the school isn't commenting on tape doesn't surprise Nathan. School leaders are hesitant to speak publicly because they haven't gotten fair or accurate media coverage in the past, he says, and they've received death threats because of that coverage.
The school's director, Asad Zaman, did speak to MPR last year. He said then a lot of the questions being raised about the school come about because Minnesotans might not be accustomed to some cultural differences.
"Most of these concerns that create an appearance of a problem would probably exist and do in fact exist in any other school with a large Muslim population, because these practices might appear foreign to some people and so would look strange or unusual."
Zaman's comments last year came after the Minnesota Education Department investigated the school and found it wasn't breaking the law. But the report found the academy needed to better separate religious expression from the school day.
In response to Wednesday's lawsuit, Deputy Education Commissioner Chas Anderson, said in a statement that they're monitoring TiZA and are currently drafting legislation to address some of the concerns that have come up.