The state has endured heavy rains over the weekend, with the town of Katherine experiencing its worst flooding since 1998.

Police evacuated more than a thousand people across the territory on Saturday, with helicopters and aircraft deployed to communities in remote areas.

"It doesn't get much bigger," police incident control acting commander Shaun Gill told journalists.

He said "at least" 90 homes were without power and warned residents against swimming in the waters.

"There is crocs absolutely everywhere. Please don't go in the water. The message is quite clear," he said.

"Don't swim in the water for two reasons: it's a fast flowing river, and also, this is where crocs are most active."

Assistant police commissioner Travis Wurst also warned residents of Katherine not to "do something silly" and jump in the water.

He warned of "crocodiles and other things that will make your life difficult".

A number of schools will remain closed into Monday due to the flooding, Northern Territory Chief Minister Lia Finocchiaro said.

More than 100,000 saltwater and freshwater crocodiles are estimated to be living across northern Australia.

The vast Northern Territory is one of the country's most sparsely populated areas and is frequently hit with extreme weather.

Researchers have repeatedly warned that climate change amplifies the risk of natural disasters such as bushfires, floods and cyclones.