The Care Quality Commission (CQC) report said it was taking enforcement action against the National Autistic Society (NAS) for improvements at Orchard House in Bideford, Devon.
During visits in September, inspectors found it was not fully safeguarding people from abuse.
The NAS said it had since made changes.
The school helps care for people with severe autism. Individual pupils often need up to four members of staff supervising them at any time.
CQC inspectors found the service user in the communal garden of Orchard House, an accommodation block for eight students aged 16 and older at NAS's Broomhayes School in north Devon.
The CQC report said centre staff told them that "the person concerned was supported by one-to-one staffing".
"Through discussion with staff it was not evident that full consideration had been given to how this person's behaviour could impact on the privacy, dignity and rights of all people using the service."
Inspectors also raised concerns that excessive or inappropriate use of seclusion and restraint had been used in some cases, including putting students who had become agitated in a bedroom and holding the door shut from the outside.
The CQC said it had found the school had failed to meet six national standards, and that it had issued two warning notices requiring the NAS to meet national regulations covering the care and welfare of people and safeguarding people from abuse.
CQC regional director Adrian Hughes said: "People are entitled to services which are safe, effective, caring, well led, and responsive to their needs.
"We expect the National Autistic Society to ensure standards are met."
The NAS said it had made changes to improve care and support, including new management and increased staff training.
It added it had also "taken the decision to close the residential and day school provision for children at Broomhayes next year to focus on a smaller service for adults".
Up to 100 jobs are believed to be under threat because of the planned closure.
Source BBC News