"It would break the end-to-end encryption and fundamentally undermines people's right to privacy. We have consistently joined civil society and experts around the world in opposing requirements that would violate the privacy of our users," the spokesperson stressed.
The company said that in the meantime, "we will also continue to engage with the government of India on practical solutions aimed at keeping people safe, including responding to valid legal requests for the information available to us".
The Indian government was yet to react to the lawsuit.
The tussle between Twitter, WhatsApp and Facebook and the union government has reached its nadir, with cops raiding Twitter offices in the pandemic earlier this week over the Toolkit controversy.
WhatsApp has gone to the court as the deadline to comply with the new IT rules meant for big social media platforms in India ended on Tuesday.
WhatsApp said that new rules infringe on users' privacy.
When the concept of "traceability" was first proposed in early 2019, dozens of organisations wrote to the Indian government about how such a provision would violate the privacy of Indian users.
The IT rules published earlier this year, in addition to calling for "traceability" risk criminal penalties for non-compliance.
WhatsApp has consistently opposed legal action that would break end-to-end encryption. The company is currently fighting the same before the Supreme Court of Brazil on a similar matter.
"We also do not believe traceability can be imposed in a way that cannot be spoofed or modified, leading to new ways for people to be framed for things they did not say or do. Such massive data collection also makes messaging platforms inherently less secure by opening up more avenues for hacking," WhatsApp had said earlier.
The MeitY had announced its draft new intermediary guidelines (IT) rules for social media platforms on 25 February.
As per the new rules, the social media platforms will have to remove offending content within 36 hours after a government directive or a legal order.
The new rules mandate that the intermediaries, including social media intermediaries, must establish a grievance redressed mechanism for receiving or resolving complaints from the users or victims.