Inspectors said the organisations are failing to work together on long-term strategies to improve support, with the relationship between some head teachers and Medway Council leaders highlighted as particularly weak.
As a result, problems faced by children with SEND are not being effectively addressed, in particular the area's high rates of exclusions among SEND pupils and a lack of specialist school provision.
"Medway's education and service leaders do not share one vision and strategy for SEN and/or disabilities," the letter to care, education and health leaders outlining the findings states.
"Local area leaders' actions to influence, challenge and work with providers across the area have had limited success.
"A considerable number of parents shared concerns with inspectors that the needs of their children are not being identified and met sufficiently well."
It adds: "The level of fixed-term and permanent exclusion is high. Effective challenge and support to some schools, initiated by the local authority, have led to a notable reduction in the number of pupils who have SEN and/or disabilities experiencing exclusion.
"However, some schools have proved hard to engage with and are not doing enough to improve outcomes for pupils at risk of exclusion."
Inspectors also found a lack of effective oversight or accountability between the council and health commissioners regarding reform of SEND, which includes replacing statements of special educational needs with new education, health and care plans.
"Council and clinical commissioning group leaders have not worked jointly at a strategic level to implement the reforms," the letter states.
"No arrangements are in place to ensure effective joint oversight and clear lines of accountability for work across education, health and care services."
Autistic children were found to be among the worst affected, having to wait between six and nine months for an assessment or diagnosis. Inspectors found the area is failing to meet national guidelines in supporting this group of children.
Despite the concerns, inspectors did praise efforts to ensure children with SEND feel safe and noted that agencies were working together to address a fear of crime among some children they spoke to.
"Children and young people who inspectors met consistently reported that they felt safe and well cared for in the settings they attend," the letter states.
"Several expressed concerns that they did not feel safe in their community as they were worried they might be at risk from those engaged in criminal activity.
"There is clear evidence of joint working and communication across agencies to ensure a clear understanding of the situation, tackle issues of concern and reduce anxiety in the local community."
Early years support for children with SEND was also praised, with inspectors noting that the proportion of this group of children reaching a good level of development had improved over 2017 and was now higher than the national average.
But due to the severity of the problems found in Medway the council and health chiefs have been ordered to present a plan to inspectors on how they will improve SEND support for children.
Andrew Mackness, portfolio holder for children's services at Medway Council said: "The welfare of our residents remains at the heart of everything we do and we will be working even closer together with Medway Clinical Commissioning Group, as well as educational establishments, to address the team's recommendations and improve outcomes for children and young people.
"We will also be working with the Department for Education and NHS England to ensure there is a joined-up approach to deliver efficient services which meet the needs of those living in our communities."