The messaging app had challenged CCI order for a probe.
Justice Navin Chawla had reserved verdict on April 13 after hearing the arguments by both the sides.
WhatsApp said the CCI jumped the gun and started the probe when this was not in fact a competition issue. The issue with respect to personal data of the users, and sharing of personalised data, was already before the Supreme Court.
The commission said it was not concerned with the privacy aspect of the issue, as the Supreme Court was already seized of it.