They are said to have been shot dead by family members earlier this week in a village on the border of the North and South Waziristan tribal districts.
The murders came after a video appeared on social media showing the girls with a young man, police said.
Two men were reportedly arrested on Sunday in connection with the case.
The two men were the father of one of the victims and brother of the other victim, police officials told BBC Urdu.
The incident is said to have taken place on Thursday afternoon at Shamplan village, in Garyom region on the border between North and South Waziristan districts in Khyber Pakhtunkhwa province, according to police.