Modi took up the matter with Mohamed during their bilateral meeting here on the sidelines of the Eastern Economic Forum, Foreign Secretary Vijay Gokhale told media persons while briefing on the meeting.
It was decided that officials of the two countries will be in touch, he said, while responding to a question on the issue in the context of India's request to Malaysia for Naik's extradition.
Though Gokhale did not elaborate, sources told that the Malaysian Prime Minister responded positively after Modi raised the issue. Since such matters are not dealt with at the leadership level, the officials of the two countries will discuss how Naik can be brought back to India at the earliest to face law of the land, they explained.
Naik is wanted in India for serious charges related to terrorism after his name cropped in connection with a ghastly terror attack at Holey Artisan Bakery in Dhaka in July 2016.
The Mumbai-born 53-year-old founder of the controversial 'Peace TV' has been living in Malaysia since 2017 after fleeing from India and the previous government there had granted permanent residency to him.
The current Malaysian government has so far not decided on sending him back to India but has barred him from delivering his public speeches.
His activities are under constant monitoring of the Malaysian authorities.
He recently made some racial comments, after which Malaysia's Home Minister Tan Sri Muhyiddin Yassin said that no one is above the country's law, "much less a permanent resident" even if he is Zakir Naik.
Naik is also facing an inquiry set up by the government of Mahathir Mohamed, who had initially said he could not accept calls to deport the preacher to India as he would be "killed" there.
Gokhale said the issue of terrorism also figured in the talks between Modi and Mohamed. He said the Malaysian Prime Minister unequivocally condemned terrorism in all forms and stated that his country was against the menace.
The two leaders discussed ways to "cope" with the growing menace of terrorism, the Foreign Secretary said.
Developments related to Jammu and Kashmir were also discussed and Modi explained the "rationale" behind the reorganisation of the state aimed at "effective governance and delivery of social justice", Gokhale said.
He said more focus in the context of Jammu and Kashmir was on terrorism emanating from Pakistan.
The two Prime Ministers also discussed the issue of trade imbalance in favour of Malaysia and Mohamed promised to address it, including by increasing imports from India.
Describing the meeting between the two Prime Ministers as very cordial, the Foreign Secretary said Modi told Mohamed that he looked forward to working with him for enhancing the bilateral ties.
The 94-year-old Malaysian leader was elected for the second time as Prime Minister in May.
( With inputs from IANS )