The 25-year-old program was run through county mental health departments and offered services required by federal law.
A spokesman for the governor said it's ultimately up to school districts to provide those services and that there was nothing illegal about the governor cutting the program with a line item veto.
Public Counsel, Disability Rights California, Mental Health Advocacy Services and law firm Gibson, Dunn & Crutcher are some of the organizations taking part in the lawsuit.
The lawsuit also names as defendants the state departments of Education and Mental Health, the Los Angeles County Department of Mental Health, the Los Angeles Unified School District and the Los Angeles County Office on Education.
About 8,000 children are affected in Los Angeles County.
The Associated Press contributed to this report.