The four-metre (13ft) creature grabbed the boy, Melas Mero, as he was fishing with his parents last Thursday at the Siloura river in Gulf province, in the south of the Pacific nation, police commander Lincoln Gerari told PNG's National newspaper.
Gerari said that police found two hands, two legs and a hip bone inside the crocodile after they tracked it down and killed it. The head was found later, and taken to a morgue.
The attack is the second to take place in PNG this year, according to a global database managed by researchers at Australia's Charles Darwin University.
The CrocBite database said a man, whose age was not given, was killed on 1 January by a saltwater crocodile at Rawa Bay, in North Bougainville.
Seventy-five crocodile attacks, of which 65 were fatal, have been recorded in PNG by the database since 1958.