Denying claims that a sense of fear prevails in the BJP, he said stories of no other senior leader apart from Modi and Shah are allowed to speak their mind are "fabricated".
The speech was made at Shahbaad Ram Leela ground in Rampur on Monday and the FIR was registered on late night on the same day.
The Congress has slammed the raids as political vendetta and alleged that the Modi government was being blinded by revenge.
The Union minister said the Army did not belong to an individual but to the nation, even as Mukhtar Abbas Naqvi was caught on camera referring to the Army as "Modiji ki sena".
The statement comes at a time when demands have been made by the Muslim community and other quarters of India to tackle rising numbers of lynchings.
In an exclusive interview with TNIE, the BJP's Muslim face also said the Narendra Modi government has worked to empower minorities.
Naqvi's remarks came a day after Prime Minister Narendra Modi used Congress leader Sam Pitroda's remarks questioning the government's aggressive action against Pakistan.
Modi's message was read out by Union Minority Affairs Minister Mukhtar Abbas Naqvi who presented a 'chadar' on behalf of the prime minister at the Ajmer Sharif Dargah.
Union ministers Nirmala Sitharaman, Ravi Shankar Prasad, Piyush Goyal and Mukhtar Abbas Naqvi, and former Madhya Pradesh chief minister Shivraj Singh Chouhan are the other members of the committee.
Murmurs of dissatisfaction have been reported among NDA allies such as Apna Dal (S) and Suheldev Bharatiya Samaj Party recently.
Talking about the opposition alliance, the Minority Affairs Minister said a big coalition was being formed against the BJP and he has been told that National Conference chief Farooq Abdullah.
Minority Affairs Minister said acts like murder are against the law but people still commit such crime and hence there is provision for punishment.
Naqvi, while referring to Shah's remarks, also said a mountain was being made out of a molehill.
There has been no increase in complaints received by the NCM over the last three years, Naqvi said to a question on whether there as been an increase in the number of complaints to the minority panel
Mukhtar Abbas Naqvi said around one lakh thirty six thousand online applications have already been received for 2019.