Ofsted found pupils at the independent Olive Tree Primary School in Luton had to ask for toilet paper and wash their cutlery in toilet sinks.
Chair of governors Dr Nurul Islam said a number of issues had been "rectified" and a formal complaint lodged over the report's findings.
Ofsted said it would investigate and took all complaints "seriously".
Inspectors found a number of standards were not met, reporting that "inappropriate books" that "did not promote British values" had been found during a previous inspection.
Despite school leaders stating the titles had been removed, the books, including some by a banned author with "extreme views about punishment by death", were still on the shelves when inspectors re-visited the establishment in November. [BBC] Read more
