The agency issued a provisional order under the Prevention of Money Laundering Act attaching mutual funds worth about Rs 9.41 crore and five bank accounts containing deposits worth Rs 1.23 crore in the name of Naik's NGO Islamic Research Foundation.
The order also attached a school building valued at Rs 7.05 crore belonging to Islamic Education Trust Chennai and a godown building in the name of Ms Harmony Media Private Limited worth Rs 68 lakhs.
The Enforcement Directorate said that it attached the assets "in view of their involvement in the case."
The central probe agency had registered a criminal case against Naik and others last December after taking cognisance of an NIA complaint filed under the Unlawful Activities (Prevention) Act.
It had also issued four summons to Naik to depose before it, but the agency said the preacher has "avoided" all of them.
"The investigations reveal that the proceeds of crime generated through the provocative speech of Naik have been either routed and transferred or utilised for the purpose other than for which they have been generated, by way of creating communal disharmony and for inciting the Muslim youths and terrorists.
"Due to the said reason, the trust/organisation IRF has been banned under the provisions of the Unlawful Activities (Prevention) Act, 1967," it said in a statement.
The agency had earlier arrested Naik's close aide, Amir Abdul M Gazdar, in this case and he is at present in judicial custody.
The ED is looking into the charges of alleged laundering of illegal funds in the case and the subsequent proceeds of crime thus generated.
The attachment of assets under PMLA is aimed to deprive the accused from taking benefits of his ill-gotten wealth and such an order gets confirmed after an order is passed by the Adjudicating Authority of the said Act within 180 days.
The National Investigation Agency had earlier registered a case against 51-year-old Naik under anti-terror laws for allegedly promoting enmity between different religious groups.
The NIA and Mumbai police had also carried out searches at 10 places in the megapolis last year, including residential premises of some of the office bearers of a foundation run by Naik. The foundation was earlier put on 'restricted list' by the home ministry for receiving funds from abroad.
Naik, who is said to be staying 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 officials of IRF for promoting enmity between different groups on grounds of religion, and doing acts prejudicial to maintenance of harmony besides various sections of UAPA.
Meanwhile, the NIA on Monday issued second summons to Naik to appear before it in Delhi on March 30.
The agency had early this month issued the first summons to him asking him to appear on March 14.
Officials said Naik has been summoned at the National Investigation Agency's headquarters in New Delhi.
The notice has been sent to the Mumbai residence of 51-year-old Naik.