Zakir, 54, was seen leaving the Bukit Aman police headquarters at 1.30 am today in a Toyota Innova.
CID director Datuk Huzir Mohamed when contacted said Zakir arrived at Bukit Aman at 3.15 pm yesterday accompanied by his lawyer.
He said Zakir was being probed under Section 504 of the Penal Code for intentional insult with intent to provoke a breach of the peace.
The preacher from India, who is a permanent resident in Malaysia, had his statement recorded for the first time last Friday for five hours.
He is alleged to have made controversial remarks against Malaysian Hindus and Malaysian Chinese during a talk in Kota Bharu on Aug 3, prompting calls for him to be deported to India.
Zakir has been wanted by Indian authorities since 2016 for alleged money laundering and inciting extremism through hate speeches.
Last Thursday police received 115 reports against Zakir under Section 504 of the Penal Code.