Elliott Dearlove, seven, got into trouble for asking a five-year-old boy at Griffin Primary School in Hull if he was “brown because he was from Africa”.
His mother Hayley White, an NHS healthcare worker, refused to sign a form saying her son had made a racist remark and now wants him to go to another school.
Miss White has said her son is inquisitive and “always likes to ask questions”.
Elliott was due to start at a new school, but his mother was told on Friday it is full.
Her MP, Karl Turner, said although protocols had to be followed, common sense appeared to “have gone out of the window”.
Mr Turner said he had been in contact with council leader Steve Brady: “I fully expect this to be resolved very soon. Steve Brady has given me assurances that the parent will be contacted by a senior officer to invite her to a meeting with him and Coun Brady to resolve this matter.
“There is a statutory provision that says schools have to take allegations of racism very seriously and deal with it appropriately.
“This is a seven-year-old child who is not old enough to form the intention of committing a criminal offence. It hardly sounds racist; it sounds like a seven-year-old being inquisitive and it sounds a fair question.
“I’d like to know if the child can’t go to the (new) school, why, and I am not prepared to put up with anything but a proper explanation.”
Miss White declined to comment. Neither Hull City Council nor the school was available to comment.