India had made a formal extradition request for Naik, who left the country in 2016, to be returned to the country after accusing him of inciting youngsters to commit terror activities through his hate speeches.
Naik, 52, in a statement published in Malaysian newspapers, thanked Prime Minister Mahathir for examining his case from an "unbiased perspective".
Mahathir, who had met the radical Indian cleric last week, has made it clear that his government will not easily give in to India's demand to deport Naik.
"We do not easily follow the demands of others. We must look at all factors before we respond," Mahathir was quoted as saying by the New Straits Times.
"Otherwise, someone will become a victim," the prime minister said in his first public comment yesterday on Naik since meeting with the hardline preacher.
Mahathir has also said that Malaysia will not deport Naik back to India, as long as he does not create problems in the country. The previous Malaysian government had granted Naik permanent resident status.
Naik, in his statement said Mahathir's decision reaffirmed his faith in Malaysia's justice and communal harmony.
"I am humbled to be a part of this diversity, and I also acknowledge the sensitivities it entails. I would never wish to disrupt or jeopardise this balance in any way or to break the rule of law of this country because it is my primary concern to foster the social harmony currently enjoyed by its citizens," he said in the statement carried by the Malaysian media.
He said that while he hoped for justice and peace to return to India, he remained indebted to Malaysia - not just as one seeking fair treatment, but as an "individual with a love of humanity".
He also claimed that over the last few years, thousands of news articles, YouTube videos and social media posts have attributed "appalling statements" to him that he did not make.
Naik is being probed under terror and money laundering charges by India's National Investigation Agency (NIA).
The NIA had first registered a case against Naik under anti-terror laws in 2016 for allegedly promoting enmity between different religious groups.
Naik is also under investigation for issuing hate speeches that inspired a deadly terror attack on a popular cafe in Dhaka, the capital of Bangladesh in 2016.