A teenage boy has been bitten on the foot by a crocodile as hundreds of people were being evacuated from flood-hit remote communities in the Northern Territory.

The 17-year-old was bitten on Wednesday as he was evacuating to a nearby town where his bite wounds were treated at a local clinic.

"There are a lot of water holes which we normally swim in ... around those communities, but just really reminding people with this, we don't know where those big crocs have got to," his local MP, Chansey Paech, told ABC Radio on Wednesday night.

"So just being water-safe and croc-wise is going to be really important in the coming months following this event."

More than 700 people from three communities will be relocated by air to Katherine and then take buses 300km north to temporary accommodation in Darwin this week.

Evacuees are expected to be housed in temporary accommodation at Foskey Pavilion and at the Centre for National Resilience in Howard Springs. It is the first time the latter will be used for emergency accommodation.

Territory authorities declared an emergency for the communities where the upper Victoria River reached major flood levels on Wednesday.

On Thursday, helicopters and small aircraft evacuated people over 17 flights, with larger aircraft from the Australian Defence Force expected to arrive as support.

Chief Minister Natasha Fyles did not say how long people would stay in Darwin for, in some cases more than 500km from their hometowns.

"We're very much in that response phase, and caring for people to make sure that we're getting them into a safe location," she said.

"That's something that we'll need to make some assessments on. Some communities will be able to to have residents go home quicker than other(s)," she said, indicating that flooding may have affected services such as power, water, sewerage and electricity.

The Victoria River at Kalkarindji surpassed the major flood level of 14 metres and was at 16.02m Thursday morning. By Thursday afternoon, the river levels had started to drop.

Authorities have urged people in the area to avoid unnecessary travel to allow for a safe evacuation.