The first cohort of Territorians have begun their journey home from the Centre for National Resilience in Darwin after being evacuated earlier this month due to severe flooding.

On Sunday morning around 50 evacuees began their trip to Kalkarindji after the Northern Territory government, community organisations and contractors worked together to restore homes, critical infrastructure and essential services.

Kalkarindji suffered comparatively less damage than Daguragu and Pigeon Hole, and repatriations to the community will continue Monday and Tuesday in stages. Evacuees from other communities will be repatriated when their homes are repaired, the NT government said.

The Kalkarindji local store has been restocked and the health centre and the school will reopen Monday. A vet and livestock inspector have been on the ground in the affected areas to provide treatments if required to animals that did not travel to Darwin with their owners during the evacuations.

More than 700 residents were evacuated to the Centre for National Resilience due to the floods which caused severe damage to Kalkarindji, Daguragu and Pigeon Hole.

Assessments of Daguragu are complete and a Waste Management Plan has been approved for implementation, with remediation works now underway.

NT Chief Minister Natasha Fyles said the government has been working in partnership with community organisations and industry to ensure evacuees return home in a safe way.

"It will be a staged approach to get evacuees home, we are making sure that power and water is available in the community," the Chief Minister said on Sunday.

"The second half of the hardship payments will also be made available once people return home to assist them in purchasing much needed items."

Pigeon Hole experienced severe flooding and remains inaccessible by road, delaying repair and repatriation activities. Residents will remain regularly informed as progress is made and will receive their second hardship payment when they return to their community.