The primary pupil - given the pseudonym Sharif Akhtar in an ombudsman's report - contracted septicaemia and almost died when his temperature rose above 38C. A healthy person's temperature ranges between 36.5C and 37.5C. Sharif has serious heart and lung problems and was born with no spleen, which makes him vulnerable to infection.
Following an investigation into whether his special needs were being properly met, Newcastle council has been ordered to pay pound;1,000 compensation.
Local government ombudsman Patricia Thomas said that school staff "considered Mrs Akhtar an over-anxious mother", but the boy had "almost died" after they failed to monitor his condition.
She was investigating a complaint from his mother that the council had failed to assess Sharif's needs and issue a statement to protect the one-to-one support provided for him.
Mrs Thomas feared the council might be operating a "blanket policy" of not statementing children with health problems, and warned this would be unlawful.
She criticised Newcastle for blaming a school which had since closed, rather than accepting corporate responsibility.
Sharif's case is one of a andful of recent reports highlighting council failings in their dealings with parents of special needs children.
Margaret McGowan, of the Advisory Centre for Education, which provides help and advice to parents, said these cases were the "tip of the iceberg".
Unless parents are very persistent, their child often does not get the help they need, she said.
"There is a feeling that if parents are pressing for extra help they are over-anxious. But time and again ombudsman cases have found in favour of the parents. They are the experts on their child."
In Salford, "insensitive and heavy-handed" officers called in the education welfare service after a mother kept her disabled son at home instead of addressing her concerns about the lack of support at school.
It took three years for the council to respond to advice from an educational psychologist and his primary school that the boy's worsening muscular dystrophy left him too weak to use pen and paper or a computer keyboard.
And in Manchester, the parents of a boy with severe learning difficulties had to commission independent reports on him before the education authority would take their concerns seriously.
The council showed a "considerable and insupportable reluctance" to acknowledge the youngster was also autistic, Mrs Thomas said.