Mohammad Asif committed the double murder in Noorshah village of Sahiwal district of Punjab province, police said today.
He had murdered his mother about five years ago but was pardoned by the family.
Police said that Asif shot his sisters during the night and fled away.
"We have launched a manhunt but he is still at large," police official Akram Sahi said.
On Monday, a father shot dead his 18-year-old daughter in Lahore after she failed to tell him where she had been for several hours, ironically on a day when Sharmeen Obaid Chinoy's documentary won an Oscar in Los Angles.
Honour-killing is a big issue in Pakistan and every year over 1,000 girls and women fall victims.