A police spokesman said the search would likely continue throughout Sunday afternoon but grave fears were held for the boy.
"Not too many people come away from a crocodile attack, I'm afraid," he said.
News Limited reports the four-metre beast was spotted on Sunday and fired on twice.
Superintendent Michael White earlier said the attack offered a grisly warning to all Territorians.
"This is a tragic circumstance for the child's family and friends and highlights the dangers of swimming in waterways in the top end," Supt White said in a statement.
The attack on the nine-year-old boy comes a fortnight after a seven-year-old girl was taken by a crocodile while she was swimming with other children and an adult at a local waterhole in the NT.
The girl was at the Gumarrirnbang outstation, 100km west of the remote community of Maningrida, when she was grabbed on November 17.
A three-metre crocodile was shot dead in the billabong the next day and the girl's remains were found inside.
-AAP