The schools watchdog Ofsted has delivered a damning indictment of the education of children with special educational needs and disabilities, warning that provision is “disjointed and inconsistent”, with thousands missing out on vital support to which they are entitled.

In her second annual report as chief inspector of England’s schools, Amanda Spielman drew attention to the plight of pupils with SEND, warning that diagnoses were taking too long, were often inaccurate, and mental health needs were not supported sufficiently.

Her report, which presents a state-of-the-nation commentary on the quality of education, revealed that in 2018 more than 2,000 of the most needy children who have official education, health and care (EHC) plans – legally binding documents setting out their needs – were still awaiting provision, almost three times more than in 2010. In 2017 the figure was more than 4,000.

The number of requests for EHC assessments that were either refused or delayed have also increased dramatically. In 2017 there were about 14,600 refusals by local authorities to carry out an assessment – a third more than two years earlier.

Spielman also raised concerns about the number of children with special needs who seemed to disappear out of education altogether. Almost 5,800 pupils with SEND left their school between years 10 and 11; some will have been removed from the school roll illegally, because they were perceived as difficult to teach or at risk of bringing down GCSE results. Half of the 19,000 GCSE-aged pupils that dropped off school rolls between 2016 and 2017 did not reappear on another state-funded school roll.

The report also flagged up a widening gap in performance and outcomes for children with SEND between the worst and best local areas. Of the 68 local area inspections carried out, there were serious failings in 30.

The chief inspector’s findings come at a time of mounting anger among parents of children with SEND who say vital support services are being withdrawn. A number of parent groups around the country have already launched legal action against their local authorities to try to resist further cuts planned for SEND provision.

A separate legal action has been launched against the education secretary, Damian Hinds, and the chancellor, Philip Hammond, whom parents accuse of failing to provide local authorities with sufficient funding to pay for SEND services for their children.

Ofsted also expressed concern about a high levels of exclusions – in secondary schools, pupils with SEND support are five times more likely to have a permanent exclusion than non-SEND children, and more than a quarter (27%) had a fixed-term exclusion last year.

While acknowledging that the quality of education and care in England is “good and improving”, Spielman’s report highlighted the “deep inequities” that remain across the education system between areas and called for urgent action to support the children still left behind.

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Addressing an audience of education professionals and policy experts in Westminster, Spielman said: “There are still children who lag behind. Children for whom it seems the die is cast, even before entering nursery, and who never catch up in 12 years of schooling.”

While sink schools have disappeared from the educational map, she said some schools had not improved for more than a decade. The report revealed there were almost 500 “stuck” schools that had been judged inadequate or required improvement at every inspection since 2005. Turnaround rates for underperforming schools “remain too low”.

“As long as children are attending schools that are perpetually less than good, we have a problem,” said Spielman. “What makes the inequity even starker is that many of these schools are concentrated in particular parts of the country, serving the same demographic groups, often the white working class.”

She said the phonics screening check had had a major impact on reading standards, but children on free school meals who reached the expected standards were 12 percentage points lower than wealthier classmates.

Spielman also made careful criticisms of government funding cuts, highlighting concerns about the financial sustainability of further education and sixth-form colleges, where spending per student is now 11% lower than for pupils at secondary school. In children’s social care, the chief inspector said while funding for statutory services had been protected, cuts in other areas such as youth services were “a false economy”.

Labour’s shadow education secretary, Angela Rayner, said: “When even the chief inspector recognises that Tory cuts to children’s and youth services are a false economy, it is time for ministers to act and end their cuts to local authorities.

Commenting on the publication of the Ofsted report, a Department for Education spokesperson said: “This report shows that standards in our schools are rising, with 86% judged to be good or outstanding compared to only 66% in 2010.

“It shows we have a robust education system – one where parents can feel assured that the vast majority of schools, early-years providers, children’s homes and local authorities provide a high level of education and care for young people, regardless of their circumstances.

“One of the key functions of a good regulator is that it highlights areas of concern and we will work with Ofsted, schools, local authorities and others to address the issues this report picks out.”