"Please convey a message to Malala, that I apologise for what my brother did to her," Rehana Haleem said, referring to the actions of her 23-year-old brother Attahullah Khan.
"He has brought shame on our family. We have lost everything after what he did. What he did was intolerable," Haleem told CNN.
"Malala is just like my sister. I'd like to express my concern for Malala on behalf of my whole family. I hope she recovers soon and returns to a happy and normal life as soon as possible," Haleem said.
"I hope Malala doesn't consider me or my family as enemies. I don't consider Attaullah my brother anymore," she added.
Police officials have said they are searching for Khan and two other men for the shooting of 15-year-old Malala, who was hit in the head by a bullet and is now being treated at a British hospital.
Since the age of 11, Malala has been encouraging people in the Swat Valley to stand up to the Taliban, who are opposed to the education of girls. Malala and two other girls were injured in the Taliban attack on Oct 9.
A day after the attack, security forces searched Haleem's house and seized documents and pictures.
They took Haleem and her family to a nearby house equipped with bars on the doors and windows, she said.
The officers asked where her brother was and whether she knew how to reach him by cell phone but Haleem told them she did not.
"I was pregnant and sick. Then, finally, after a day or two, they released me and my husband and told me they were letting me go only because I was sick," she said.