Research undertaken by the two charities and funded by the City Bridge Trust, found that councils offer little support to children affected by domestic violence, particularly those deemed to be below "high risk" thresholds for child protection intervention.
The report revealed that some areas offer no services to children living with domestic violence, while others consider children’s needs as second to mothers.
It also found that domestic violence risk assessments are rarely used to identify the needs of children, and that children are often considered separately from their mothers in terms of support.
According to the charities, current policy can compound the problems of children trying to escape abuse. For example, boys over the age of 16 are not permitted to live in refuges with their mothers, in some cases leaving them homeless or remaining with a violent adult.
Refuge and the NSPCC are now calling on every council to provide support services specifically targeted at children affected by domestic violence, and for more specialist domestic violence training for professionals.
The charities also want children to be consulted on the design of services that directly affect them, as well as clearer guidance for the police on talking to children separately from parents at domestic violence incidents.
Sandra Horley, chief executive at Refuge, said the lack of services for children affected by domestic violence is frustrating, given that charities have been campaigning to raise awareness of the needs of children exposed to domestic violence for decades.
"Identifying a funding stream that allows organisations like Refuge to provide integrated and equal services for abused women and their children often feels like the search for the Holy Grail but it must be found if we are to provide long term effective solutions for these families," she said.
NSPCC chief executive Andrew Flanagan, added: "Gaps in services come from gaps in knowledge. It is only through listening to children living in homes with domestic violence or with a mother who has fled violence that shortfalls in keeping children safe can be addressed.
"These children have witnessed or continue to witness severe abuse. Any resulting negative psychological and social impacts can be reduced with the right support. But services will never get it right if they never ask children and young people what they actually need and want."