Special education students at a Brooklyn charter school did not get mandated services and were punished for behavior that arose from their disabilities, according to a lawsuit filed in federal court on Thursday.

The suit, filed on behalf of five students at Achievement First Crown Heights, described a “systemic failure to provide them a free appropriate public education, in violation of their rights.” It said that students did not get physical therapy and other services for weeks at a time, and that a student with autism was disciplined for not looking in the direction a teacher instructed or for hiding under his desk.

In addition to the charter network and the school, the suit also named the New York City Department of Education and the New York State Education Department, asserting they failed to make Achievement First, a network with schools in Connecticut and Rhode Island as well as in New York City, live up to its responsibilities.

“Kids with special needs not only should be granted accommodations for their needs, but they must be under federal and state law,” said Michelle Movahed, a senior staff attorney at New York Legal Assistance Group, a nonprofit group that is representing the students and their families. “This is not just a question of doing the right thing.”