After a person is declared a 'fugitive economic offender', the prosecuting agency is vested with the power to confiscate all his assets and properties to recover the dues.
EAM S Jaishankar said Naik's extradition issue had indeed come up during prime minister Modi's meeting with Malaysian counterpart in Vladivostok.
Naik, who has been living in Malaysia for the last three years, is facing charges of inciting communal disharmony and committing unlawful activities in India.
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.
Naik, wanted by Indian investigation agencies in terror-related cases, is currently living in Malaysia.
Naik has also defended the terrorist organisation Islamic State and batted for men's 'right' to beat up their wives, the Indian agencies have alleged.
Islamic preacher Zakir Naik apologises to Malaysians for race remarks; police bans his public activities
On Tuesday, Zakir Naik said in a statement his detractors had taken his remarks out of context and added strange fabrications.
Naik is alleged to have made controversial remarks against Malaysian Hindus and Malaysian Chinese during a talk in Kota Baru on August 3, prompting calls for him to be deported to India.
Islamic preacher Zakir Naik had asked the Malaysian Chinese to 'go back' first, as they were the 'old guests' of the country, during a religious talk in response to calls for his own deportation.
Malaysian Human Resources Minister urges action against Zakir Naik for denigrating Hindu Malaysians
The move comes after Zakir had recently alleged that the Hindus in Malaysia are more loyal to Prime Minister Narendra Modi than Mahathir Mohamad.
The court warned that if Naik fails to appear before it by July 31, a non-bailable warrant will be issued against him.
Spokesperson of the External Affairs Ministry Raveesh Kumar also asserted that the fairness of the Indian justice system has never been in question.
The Islamic preacher, who is now living in Malaysia, said that while he has trust in the Indian judiciary, he had no faith in the prosecution system.
The 53-year-old radical television preacher reportedly left India in 2016 and subsequently moved to Malaysia, where he was granted permanent residency.
The agency said its probe found that the total quantum of funds received in the bank accounts of IRF, from 2003-04 to 2016-17, is to the tune of Rs 64.86 crore.