Police said locals on the outskirts of the town of Tabubil, in Western Province, woke on Thursday to the screams of the baby.
Beset with the grisly sight of the father allegedly eating his child, an angry mob chased him to the police station where he was detained after a short struggle.
Police said the discovery was too late to save the baby, who died of his injuries.
Tabubil police commander Demas Tapea said officers had detained a man and his wife to assist them with their inquiries.
"It is a very disturbing incident," Sergeant Tapea said.
"The community is upset, angry but there is also a lot of fear and anxiety because there is a belief in sorcery or witchcraft."
Sgt Tapea said the main suspect was known to police.
"Locals are saying the man was carrying out a sorcery ritual, or initiation, to become part of some sort of special society," he said.
"The suspect has a long history of drug abuse and we are not surprised something like this has happened.
"A few years ago, he went crazy in what we believe was due to the effects of drugs," he said.
In 2009, it was estimated at least 50 people were killed that year in sorcery-related murders in sudden or unexplained deaths in isolated communities.
© AAP 2011
"Ladies in mourning "
© Kieron Nelson 2011 "Vanishing Cultures Photography"