He cited public order and religious sensitivities as the reason not to allow the Mumbai-based preacher to deliver his speech.
The preacher is supposed to hold a talk at Universiti Teknikal Malaysia Melaka (UTeM) on this Sunday.
He is supposed to deliver a talk titled "Similarities Between Hinduism & Islam".
Promotional video for Dr Zakir's lecture tour in Malaysia - Source: Dr. Zakir Naik YouTube Channel
Yesterday, the MIC Youth had lodged police reports regarding the talk and called on the police not to allow the programme to take place.
MIC Youth chief C. Sivarraajh said the wing was disappointed with UTeM for inviting Dr Zakir.
"Zakir Naik is known for his demeaning tactics to undermine other religions that could spark unrest without weighing the respect and sensitivity of others," he said in a press statement.
Sivarraajh said Dr Zakir is banned in the United Kingdom and Canada for allegedly spreading teachings that could create violence and terrorism.
"The government and religious affairs department should consider the sensitivity of his topic in staging a comparison between Muslim and Hinduism," he said.
The wing also planned to handover a memorandum to the Home Minister and Khalid later today, urging them to stop the programme.
Perlis Mufti Dr Mohd Asri Zainul Abidin, popularly known as Dr MAZA, last Saturday had said millions of Muslims have benefited from Dr Zakir's lectures.