The Post-Courier newspaper said police were present during the killings last week but were outnumbered by an angry mob and could do nothing to prevent the grisly deaths.
"We were helpless. We could not do anything," Bougainville police inspector Herman Birengka told the paper, saying his officers were threatened when they tried to negotiate the women's release.
According to Birengka, who described the murders as "barbaric and senseless," the women were taken captive last Tuesday by relatives of a former school teacher who died recently.
"The two women were rounded up and taken to Lopele village after they were suspected of practising sorcery and blamed for the death of the former teacher, who was from Lopele village," he said.
They were tortured for three days, suffering knife and axe wounds, before being beheaded in front of the police who had been sent to the village to mediate, the report said.
The killings come just days after another report that six women accused of sorcery were tortured with hot irons in an Easter "sacrifice" in the Southern Highlands.
Last month, a woman accused of sorcery was stripped naked and burned to death by a mob, with Amnesty International stepping up calls for an end to sorcery-related violence in Papua New Guinea.
Amnesty has urged the government to stamp out the practice in the Pacific nation where there is a widespread belief in sorcery and where many people do not accept natural causes as an explanation for misfortune and death.
There have been several other cases of witchcraft and cannibalism in PNG in recent years, with a man reportedly found eating his screaming, newborn son during a sorcery initiation ceremony in 2011.