Amid growing calls that his Islamic Research Foundation (IRF) should be banned, Naik urged the government to be "fair" in its investigation and be "truthful with facts".
In a 2,000-word open letter, Naik said he was ready to be punished for any wrongdoing but this should be on the basis of concrete evidence and not hearsay.
"If you find any wrongdoing on my part, punish me by all means. Give me the harshest of punishments if I've wronged anyone.
"My appeal to the government - be fair in your investigation. Be fair in what you allege. Be truthful with facts. To my fellow citizens - Let no one and nothing dissuade you from speaking the truth," he said.
He said he had spent 25 years promoting peace and spreading greater awareness of Islam besides talking about similarities between religions, and the last two months had been a rude shock.
"I am alarmed at the murder of democracy and strangulation of fundamental rights... I am also alarmed at how the system, media and the agencies are being used to suit a pre-meditated end result set by none other than our own governments," he wrote.
Saying the Constitution gave him freedom to profess, practice, and propagate his religion, he claimed there was "a deeper agenda behind this vicious campaign" against him.
This, he said, was not only an attack on him "but an attack against Indian Muslims".
In case he and IRF are banned, he said: "If you thought intolerance increased in the country recently, this action of the government will take it to an all-time high."
Naik claimed that selective government documents were being selectively leaked to the media.
He rubbished accusations of forced conversions against him and his NGO, asking for the "converted person" and his or her statement about how he or she was forcibly converted to be made available.
Naik, whose sermons are alleged to have turned some young Muslims into radicals, said he may find shelter in other countries.
"... but this isn't only about me. It's about us. It's about the morals and values of a great country.
"What will become of India if we let bigotry and injustice seep into the very fabric of our nation?" he said.
Naik has been on the radar of security agencies for long and his channel Peace TV has been banned in India for broadcasting "objectionable" content.
