The boy was swimming with friends in the Mudginberri Billabong in the Northern Territory's Kakadu National Park yesterday 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 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 croc responsible was between 2-3 metres.
Two crocodiles were shot and cut open overnight, but they had not ingested any human remains.
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"One 4.3 metres; one 4.7 metres," Sergeant Stephen Constable said of the creatures.
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 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 late today and prepared to continue searching the waterways by boat through the night, though Constable said efforts would be scaled back.
Parks officer and crocodile specialist Garry Lindner said a 2-3 metre crocodile was sizeable, particularly up against a child.
Lindner 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.