"The proposed changes raise grave concerns regarding the implications for the choice and autonomy of Indian citizens," said the tech ministry's email addressed to WhatsApp boss Will Cathcart dated Jan 18, which was reviewed by Reuters.
"Therefore, you are called upon to withdraw the proposed changes."
WhatsApp did not immediately respond to a request for comment but has previously said that its new privacy policy update does not affect the privacy of users' messages with friends, family and in groups.
The company last week said it would delay the new policy launch to May from February, after facing a raft of criticism over the new terms including in its biggest market of India.