The inspectorate's annual report for 2017/18 highlights a series of concerns about the quality of support for children with SEND.
It warns that education, health and care (EHC) plans for children with SEND are too variable, adding that many areas offer sub-standard provision.
Almost half (30) of the 68 local areas inspected for SEND provision were asked by Ofsted to provide a written statement of action due to concerns raised by inspectors.
This patchy service is widening the gap in terms of good life chances between children with SEND and their peers, the report warns.
The report adds that in 2018 there were 2,060 children with an EHC plan, or a statement of special need which preceded the plans, who were awaiting provision - almost three times more than in 2010.
"One child with SEND not receiving the help they need is disturbing enough, but thousands is a national scandal," Ofsted chief inspector Amanda Spielman said.
The report also highlights an increase in the number of refusals by councils to carry out an assessment - something they can do if they believe a case has not met the required threshold of needs. In 2017 there were around 14,600 refusals for an assessment of SEND, a third more than in 2015.
The high number of SEND pupils being excluded by schools is another concern raised. This includes concerns that some are being "off-rolled", whereby schools seek to boost their performance figures through tactics such as encouraging parents of challenging or underperforming pupils to take up home-schooling.
Pupils with SEND support are five times more likely to have a permanent exclusion than those no SEND, the report states. Between January 2016 and January 2017, 19,000 pupils dropped off school rolls between year 10 and year 11. Around 5,800 of them are children with SEND, with Ofsted's report suggesting "some of them may have been off-rolled".
Overall children with SEND make up 30 per cent of those who leave their school, despite only accounting for 13 per cent of all pupils.
Spielman said: The exclusion of pupils for the purpose of boosting a school's performance figures is unacceptable and schools that are off-rolling children have clearly lost sight of the purpose of education."
Jolanta Lasota, chief executive of the charity Ambitious about Autism said Ofsted's report shows that children with SEND are "being badly failed".
"It is wrong that children are not receiving the support that they are entitled to in their education, health and care plan, she said.
"It is wrong that official exclusions of autistic pupils have increased by nearly 60 per cent in five years, compared to only four per cent for all pupils.
"It is wrong that illegal gaming of the system - off-rolling - means that thousands of children with autism and SEND are missing from school.
"The current system favours exclusion over inclusion, and children and young people are being denied an education simply because they're autistic. It's time for real accountability and enforcement."