Police have confirmed the death of a 12-year-old Indigenous boy attacked by a crocodile at Kakadu National Park in the Northern Territory.

Acting Commander Michael White said search teams had located evidence that "strongly indicated" the boy had died in the attack.

He said DNA testing would be carried out to confirm the identification but that it had become a matter for the coroner.

"No specifics will be given in relation to the trauma or type of evidence located, out of respect for the family," he said.

The boy's family has been informed and the local community is grieving.

Police and rangers had been searching for a crocodile that attacked a group of five boys swimming in a billabong at Magela Creek, behind the Mudginberry outstation, on Sunday.

Sergeant Stephen Constable has been leading the search for the missing boy since then. He says a helicopter rejoined the operation at first light today.

Boat crews were told to shoot any saltwater crocodiles of between two metres and 2.5 metres spotted in the area.

This was based on measurements of bite marks on the arms of a boy who survived the attack.

Sergeant Constable says police shot a 2.5-metre crocodile overnight and have set a trap for another that was sighted.

Three crocodiles have now been killed in the hope of finding any clues as to what happened to the missing boy.

Call for review of crocodile management

An Aboriginal corporation representing traditional owners in Kakadu National Park is calling for a review of crocodile management around their communities.

The Gundjeihmi Aboriginal Corporation says the Mirarr people and other traditional owners have managed the land for tens of thousands of years, compared to the Commonwealth's 30 years.

It says the Federal Government must listen to the advice of local people and review crocodile populations and safety concerns.

Corporation spokesman Justin O'Brien says it is only in recent decades that crocodile attacks have become an issue.

He says over-management of the park has led to more crocodile-related incidents.

"Our senior traditional owner Yvonne Margarula has told me she would swim just here at Mula Island billabong when she was a girl in the 1970s and '80s," he said.

"The [crocodile] numbers were low and, importantly ... crocodiles had a fear of humankind.

"Over the past 40-plus years since the protection laws have been in place, all that has changed."

Culling would create more problems, expert says

But a Darwin crocodile expert says culling is not the best way to stop crocodile attacks in the Northern Territory.

Crocodylus Park chief scientist Charlie Manolis says it would create more problems than it would solve.

"I always worry a little bit about just going in and ... trying to cull and reduce numbers," he said.

"What that does with a lot of salties is they will just go to ground and you won't see them at all.

"It may give people a false sense of security."

Mr Manolis says data collected over 30 years shows crocodile populations in some rivers are increasing slowly.

"But the biggest thing is that the average size of crocodiles is getting bigger and bigger and bigger," he said.

"The average saltie might be 3.5 metres, four metres long now, whereas 20 years ago they might have only been one and 1.5 metres long.

"They might not be increasing so much in numbers but their average size is increasing."

He says more education about crocodile safety is needed for Indigenous communities in remote areas.

He says recent research shows a high proportion of crocodile attacks in the Territory have involved Indigenous people.