SYDNEY (AFP) - Police and rangers on Monday hunted for a crocodile that snatched a 12-year-old boy from a northern Australian waterhole, with shoot-to-kill orders for any creature longer than two metres and fresh calls for a cull.

The boy was swimming with friends in the Mudginberri Billabong in the Northern Territory's Kakadu National Park on Sunday afternoon when the group was attacked.

One other boy suffered bite wounds as he tried to fight the creature off.

Aerial, land and boat searches in and around Magela Creek, which feeds the billabong or waterhole, continued throughout the night but there was no sign of the boy.

The NT Parks and Wildlife Commission gave rangers the order to shoot dead any crocodile longer than two metres sighted in the area of Mudginberri Outstation, which is about 200 kilometres east of Darwin.

The order had originally been for animals bigger than three metres but was expanded after examination of the bite marks on the boy who escaped revealed that the crocodile responsible was between 2-3 metres.

Two crocodiles were shot and cut open overnight, but they had not ingested any human remains.

"One 4.3 metres; one 4.7 metres," Sergeant Stephen Constable said of the creatures.

"We've since had a look at both crocodiles and neither of them had anything in their stomachs."

The local Aboriginal people, the Mirarr, called for a cull of the predatory reptiles around Jabiru following the incident.

"Mirarr traditional owners are saying (it's) high time to cull crocodiles," said Mr Justin O'Brien, chief of the Gundjeihmi Aboriginal Corporation.

There are periodic calls for crocodile culls after fatalities in the Northern Territory but their numbers are such that it's historically been considered impractical.

Rangers set a trap in Magela Creek on Monday and prepared to continue searching the waterways by boat through the night, though efforts would be scaled back.

"We've done the sprint, now we've got to pace ourselves," Sergeant Stephen said.

Parks officer and crocodile specialist Garry Lindner said a 2-3 metre crocodile was sizeable, particularly up against a child.

He said flooding due to the local monsoon season was complicating the search, leaving the 200-metre waterway more than a kilometre wide.

Saltwater crocodiles can grow up to seven metres long, weigh more than a tonne, and are a common feature of Australia's tropical north.

Their numbers have increased steadily since the introduction of protection laws in 1971, with government estimates putting the population at 75,000-100,000.

The most recent fatality was in August last year, when a man was taken by a 4.7-metre croc as he swam across the Mary River.

Parks officials said the Magela Creek area was well signposted as a crocodile danger zone.

"We have big croc warning signs with croc jaws and a big thing saying 'croc risk; do not swim here, do not enter'," a spokeswoman said.

Australian researchers launched the world's first crocodile attack database, CrocBITE, last month, hoping to firm up anecdotal reports that harmful or fatal incidents are increasing.

Sunday's attack in Kakadu is the 11th fatality recorded so far this year by the CrocBITE team, which is based at Australia's Charles Darwin University.

The other crocodile-related deaths in 2014 have been in Angola, East Timor, India, Indonesia, Namibia, Papua New Guinea, South Africa, Zambia and Zimbabwe. Five have involved saltwater crocs.