The organisation employs 3,000 staff and volunteers in 300 locations across Kildare, Wicklow, Dublin, Meath, Louth and Kerry.
St John of God Community Services will not transfer to the HSE after an agreement was reached on funding.
8,000 children and adults receiving intellectual disability and mental health services will continue to do so as currently provided.
The HSE and St John of God Community Services held intensive discussions over funding, and also agreed a timeline for final decisions relating to an historical deficit.
The organisation employs 3,000 staff and volunteers in 300 locations across Kildare, Wicklow, Dublin, Meath, Louth and Kerry.
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