Unite is looking to ballot its members at the House on the Hill project, Lewisham, over possible strike action concerning the dispute, which centres on new contract terms being offered to staff.
The union says that staff contracts were terminated last December and is concerned that replacement deals offer inferior pay and annual leave entitlement.
This comes on top of a 14-month dispute between the charity and the union over weekend working at the project, which offers residential care to children.
A spokeswoman for Action for Children refused to discuss details of the dispute but confirmed that "negotiations are ongoing."
Rachael Maskell, Unite national officer for community and not for profit workers, said: "Employees are feeling totally demotivated and fed up by the way they have been treated by Action for Children."
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