A report by the ombudsman about the education, health and care (EHC) plan process reveals it is now upholding nearly nine out of every 10 (87 per cent) cases it investigates - compared with 57 per cent across all cases it looks at.
In 2018/19 the ombudsman received 45 per cent more complaints and carried out 80 per cent more detailed investigations about EHC plans than in 2016/17.
It found that serious issues include severe delays of up to 90 weeks when issuing a plan, a requirement for the process to take no longer than 20 weeks.
It also warned of "poor planning and anticipation of needs", such as council areas without any specialist provision available to them, poor communication and preparation for meetings - including regular stories of non-attendance and no, or insufficient, paperwork being submitted, and inadequate partnership working - with EHC plans regularly issued without advice from health or social care services.
It also criticised a lack of oversight from senior managers, with cases "drifting needlessly" and "attempts to farm out responsibilities to parents".
Ombudsman Michael King described the situation as "exceptional and unprecedented in our work".
"Two years ago when the system was bedding in, we were concerned we were upholding around 80 per cent of investigations," he said.
"That we are investigating and upholding significantly more complaints two years later suggests a system in crisis.
"I am now particularly concerned some authorities may be putting in place extra barriers to ration scarce resources, rather than basing support on children's needs. While I can empathise with the difficulties authorities face, there can never be an excuse for failing to meet the statutory rights of children.
"I hope this report puts the children and their families' experiences in the spotlight and the battles they face, and ultimately more urgency on the whole SEND system improving."
Last month, the National Audit Office warned that children with SEND are not getting the support they need as councils and schools battle to cope with the twin threat of rising demand and funding pressures.
The government has said an extra £700m will be made available for children with SEND as part of a wider £14bn schools funding pledge over the next three years and has committed to a major review of the system.
A Department for Education spokesman said: "As the ombudsman admits, this report is based on a very small sample size - covering less than 0.3 per cent of all cases in 2018.
"Over 48,000 children were issued with new education, health and care plans in last year, and the majority of these were completed within 20 weeks. During the assessment process children continue to attend their school and receive additional support, until their tailored support package is put into place.
"We've also announced an extra £700m for pupils with complex needs in 2020/21 - an 11 per cent increase on this year.
"However, we know the system is not working well enough for every family, and have launched a review to introduce further improvements."
Meanwhile, an inspection of SEND provision in Middlesbrough found that the area has made sufficient progress in addressing serious weaknesses highlighted in a previous visit.
"There is now greater collective ambition for children and young people who have SEND," a letter outlining the findings states.
"Crucially, local area leaders have secured the strong support of frontline staff who share their commitment to improving the outcomes achieved by this group of children and young people."