Police also stated that the televangelist had floated four shell companies in which his kin are directors.
According to an official attached to Economic Offences Wing (EOW), they are probing the motive behind floating the shell companies.
"Was it (founding of shell companies) meant to integrate funds....or what activities these funds were to be used for," he said.
The official said the money trail involving the foreign funding and its transfer in bank accounts of Naik's kin will now be probed under the Foreign Contribution (Regulation Act).
He refused to elaborate on the exact period when Rs 60 crore was deposited in Naik's account and the year when the shell entities were founded.
The Mumbai Police, tasked with probing Naik's alleged provocative speeches, had submitted its report to the state government on Tuesday.
Police were asked to probe Naik's speeches available online to see if any of them could have encouraged youths to join terrorist groups, amid reports that his preachings inspired some of those involved in the Dhaka terror strike.
"Mumbai Police found Naik to be allegedly involved in unlawful activities with possible terror links," Chief Minister Devendra Fadnavis said on Tuesday.
He had said his government was examining the report with several aspects that are in the domain of the Centre, and that he will send it to the Home Ministry for further action.
The CM had also said efforts would be made to extradite Naik, currently abroad, if he failed to return on his own.
The city police is also conducting a joint inquiry (with other agencies) into the functioning of Naik's Islamic Research Foundation (IRF), to scrutinise the finances it has received from various parts of the world.
Naik, in a media interaction via Skype from Saudi Arabia last month, had rubbished allegations against him while terming himself as the "messenger of peace".