Senior Advocate Kapil Sibal, appearing for WhatsApp, told the court that as per his client's stand the accounts of those not accepting the new policy will not be deleted for the time being.
WhatsApp's statement comes against the backdrop of an affidavit filed by the Centre in the court earlier in the day.
Sibal added that although the accounts would not be deleted right away, they will eventually be removed if the guidelines were not accepted.
The company did not clarify the reason behind the decision and did not divulge the number of users who have accepted the terms so far.
WhatsApp told the bench that private conversations of individuals are protected by end to end encryption.
A thorough and detailed investigation is required to ascertain the full extent, scope and impact of data sharing through involuntary consent of users, the CCI said in an order issued on Wednesday.