The departure of Mr Stone, a former federal Liberal party president and former Liberal chief minister of the Northern Territory, was widely expected.

The Minister for Emergency Management, Murray Watt, announced that Mr Stone will take leave from his role as agency coordinator-general on Friday before ceasing his employment on August 31.

"I would like to thank Mr Stone for his service in establishing and leading the NRRA since its inception," Senator Watt said in a statement.

READ MORE

Before the election there were calls for him to resign after appearing to blame the flood victims in NSW and Queensland who had attacked the government's emergency response.

"You've got people who want to live among the gum trees, what do you think is going to happen? Their house falls in the river, and they say it's the government's fault," Mr Stone told Nine newspapers.

As flagged, the agency has moved to sit within the Home Affairs portfolio alongside Emergency Management Australia - the agency which deals with situational awareness, emergency preparedness, crisis management and response.

Senator Watt has announced that, from September 1, the two agencies will merge to form a new organisation called the National Emergency Management, Resilience and Recovery Agency or NEMRRA.

Home Affairs chief operating officer Justine Saunders will serve as acting NRRA coordinator-general until the establishment of the proposed new agency.