"I am happy to know that my son's innocence is being proved," Gopinatha Pillai told a TV channel from his home at Thamarakkulam near Mavelikkara in Alappuzha district.
Pillai said he believed that justice would be delivered in the case.
An ex-service person, Pillai said the charge sheet filed by CBI gave him hope that his son's innocence would be proved as he had always held.
"I always believed that Modi was aware of the encounter," he said.
The central probe agency, in its charge sheet, said that 19-year-old Ishrat Jahan was killed in a "fake" encounter in 2004. Seven police officers were charge sheeted in the case.