The Kashmir bandh call was given by Majlis-e-Mushawaraat and the victims' families to get justice for the Neelofer and Aasiya.
Mohd Shafiq Khan, member of the Majlis-e-Mashawarat said, "This is a systematic cover-up. So we have no faith in Indian investigating agencies, and for that matter in no institution of India now."
The CBI submitted the 66-page probe report before the Jammu Kashmir High Court on Dec 14.
According to the CBI report, the Shopian deaths occured due to drowning and the whole story of rape and murder was fabricated.
The CBI has filed a chargesheet against 13 people for fabricating evidence, including six doctors and five lawyers.
The CBI has also given a clean chit to the police officers who were accused of destroying evidence.
The families of the victims have refused to accept the CBI report, alleging that the agency conducted a partial probe.