On April 25, 2025, the Union government filed a 1,332-page affidavit in the Supreme Court, seeking dismissal of petitions challenging the Waqf (Amendment) Act, 2025’s constitutional validity. Filed by Shersha C Shaik Mohiddin, Joint Secretary, Ministry of Minority Affairs, the affidavit argues the Act regulates secular property management without infringing religious freedoms under Articles 25 and 26. The Centre refuted claims that removing "Waqf-by-user" protections harms undocumented Waqfs, emphasizing mandatory registration since 1923.

It highlighted a "misleading narrative" and noted a 20.92 lakh hectare increase in Waqf land post-2013. The government opposed staying the Act, citing legal precedent against halting statutory provisions. On April 17, it assured no denotification of Waqf properties or appointments to Waqf bodies until May 5, when the Court, led by Chief Justice Sanjiv Khanna, will hear interim orders.