Agency officials said they had summoned representatives of Islamic Research Foundation (IRF) last week and following their deposition on Tuesday, the Investigating Officer (IO) of the case will record the statement.
They said certain documents sought by the IO will also be scrutinised.
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ED is looking into the charges of illegal funds laundered by the accused and the subsequent proceeds of crime thus generated.
The agency has already scanned some documents showing "doubtful" banking transactions.
The National Investigation Agency (NIA) had last month registered a case against 51-year-old Naik under anti-terror laws for allegedly promoting enmity between religious groups.
After registering the case against Naik and IRF, the NIA along with Mumbai police had carried out searches at 10 places in the megapolis, including residential premises of some of the office bearers of IRF, which was earlier put on restricted list by the Union Home Ministry for receiving foreign funds.
Naik, who is in Saudi Arabia to evade arrest after some perpetrators of the Dhaka terror strike last year claimed they were inspired by him, has been booked along with unnamed IRF officials under section 153-A of IPC (promoting enmity between different groups on grounds of religion and doing acts prejudicial to maintenance of harmony) and sections of UAPA.
The charges levelled by the NIA also include those under sections 10 (being member of an unlawful organisation), 13 (punishment for being member of illegal organisation) and 18 (punishment for being involved in a conspiracy for committing any terror act) of UAPA.
IRF came under the scanner of security agencies after one of the terrorists involved in the Dhaka cafe attack allegedly posted on social media he was inspired by Naik's speeches.
Maharashtra Police has also registered criminal cases against Naik for his alleged involvement in radicalising Muslim youth and luring them into terror activities.
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