They are said to have been shot dead by a family member earlier this week in a village on the border of the North and South Waziristan tribal districts.
The killing occurred after a short mobile video of them with a young man surfaced on social media, police said.
Police have been sent to the remote area to investigate the case.
The incident is said to have taken place on Thursday afternoon at Shaam Plain Garyom, a border village of North and South Waziristan in Khyber Pakhtunkhwa, according to a police report quoted by Pakistani daily Dawn.
It said the reason behind the killings of the two girls, aged 16 and 18, was believed to be a video, provided to Dawn, which shows a young man recording himself with three young girls in a secluded area outdoors.
It appeared the video was shot nearly a year ago and most probably went viral on social media a few weeks ago, a senior police official told the newspaper.
"At the moment, our topmost priority is to secure the life of the third girl and the man before taking any action," the officer said.
Human Rights Watch says that violence against women and girls remains a serious problem in Pakistan.
Activists believe about 1,000 such "honour killing" murders are carried out across the country every year.
What is an 'honour killing'?
It is the killing of a member of a family who is perceived to have brought dishonour upon relatives.
Pressure group Human Rights Watch says the most common reasons are that the victim:
- refused to enter into an arranged marriage
- was the victim of a sexual assault or rape
- had sexual relations outside marriage, even if only alleged
But killings can be carried out for more trivial reasons, like dressing in a way deemed inappropriate or displaying behaviour seen as disobedient.