The family of Sherish and Farzana said two men on motorcycles came to their house in Jaranwala in Punjab, saying they were unwanted in Muslim lands.
It's claimed the men shouted they were relatives of those who raped the girls. They're calling on the family to drop the legal case against the men who are currently awaiting trial.
The family said after much prayer the gunmen left, leaving them to flee to a nearby church where they've taken refuge.
Speaking about the incident, the girls' father Ilyas Masih said: "I wish never to go back. We already paid a big cost of my daughter's honour, we can't afford the loss of any family member now."
The church leader has since contacted his bishop who is working with police to secure their safety.
Wilson Chowdhry of the British Pakistani Christian Association is calling on believers to pray.
Speaking on Premier's News Hour, he said: "Pray for the safety of the family. The girls have undergone such a brutal attack.
"They're suffering regular intimidation. The family have been ostracised by the community simply because they are Christians.
"They need to find a long term solution for housing and to be counselled out of the depression they've found themselves in. This kind of attack has only made their demoralised status increase."
Hear more from Wilson Chowdhry speaking to Premier's Des Busteed on the News Hour: