First Nations communities affected by floods in Western Australia, the Northern Territory and Queensland will receive extra mental health funding the federal government announced Friday.

The National Aboriginal Community Controlled Health Organisation (NACCHO) will receive $4.8 million to boost mental health services for First Nations communities impacted by these floods.

Funding will be distributed amongst 13 Aboriginal Community Controlled Health Organisations to deliver culturally appropriate trauma counselling and mental health support.

Earlier this year flooding due to ex-tropical Cyclone Ellie impacted parts of the Kimberley and the Top End. Heavy rains meant water levels were at a record high in Fitzroy Valley, at 17m high in Fitzroy Crossing. The floods resulted in the river engulfing the main bridge and shattering it.

In the Northern Territory, more than 700 residents were evacuated as the floods caused severe damage to Kalkarindji, Daguragu and Pigeon Hole.

Assistant Minister for Indigenous Health, Senator Malarndirri McCarthy said floods are "particularly devastating" for remote communities.

"Flooding is an awful experience for any community, causing emotional distress and mental health issues," she said.

"For remote First Nations communities it can be particularly devastating as they are isolated from their kin, displaced from their homes and removed from Country.

"This extra funding will allow local community-controlled health services to provide much-needed mental health support, so these communities can rebuild and recover."

NACCHO will retain some funds to respond to any emerging mental health needs in flood-affected communities, and to work with other service providers to ensure holistic, comprehensive health care is available to local communities.