The National reported the morgue at Mendi Hospital in Southern Highlands province was raided in the middle of the night last Saturday.
Provincial police commander Martin Lakari said the raiders threatened to kill the mortuary keeper before taking the remains of two women and a man.
The bodies were found in the Mendi River over the New Year period.
Mr Lakari told RNZ Pacific that police suspected they had died from sorcery-related violence because they were not reported missing.
