Spokeswoman Sandy Catt says Mint Valley Elementary School stopped using the box Wednesday in response to complaints that came in after a photo of the box was posted on Facebook.
Nine children with behavior problems used the padded booth.
Supporters in the district and the state say the seclusion rooms can be helpful tools to help children deeply affected in the autism spectrum and that they can help kids calm down and not hurt themselves or others.
Other districts in the state use similar-type rooms, but the state doesn't know how many because the rooms are regulated by the individual school districts.
And many parents aren't happy with the concept.
Jim and Mandy McCracken say they never gave permission for their 7 year old daughter to be placed inside a seclusion room inside Elma Elementary -- which they say happened for 3 1/2 hours in October.
"When she came out of there, she looked like a zombie," Jim McCracken said. "I tried to talk to her; she would not talk to me. It's really hard on a kid that has autism."
School leaders say the autistic second grader was acting up, so she was placed there with a staffer.
"We have to make decisions based on the safety of the student, the safety of other students, and the safety of the staff, just like every other school would do," said Elma School Superintendent Howard King.
But King says the students are never left alone in there.
"At no time is that room used for just the student, him or herself. There's always an adult there," King said. "The claim that she was by herself is totally untrue."
State law allows for the use of isolation rooms for students who are receiving special education services and there are special conditions -- they have to be lit, and well ventilated, there has to be visual access, and restraints can't affect breathing.
Nathan Olson, who is the communications manager for Office of Superintendent of Public Instruction, says there is no provision in state law to put students who are not in special education in those rooms.
"If that's the case, that is wrong," Olson said. "And if that's the case, we would like to hear about that."
The McCrackens filed a complaint against their Elma school.
"They should not be allowed to just do this without the permission of the parents," Jim McCracken said.
The state says it needs more information.