Darul Uloom Deoband is an Islamic school propagating Sunni Islam in the Indian Subcontinent.
Akhtar, who has recently become a Rajya Sabha MP, said he received an anonymous email that said 'countdown' to his 'end' has 'begun'.
The email also challenged him to 'save' his life if he can.
"I immediately called up Maharashtra anti-terrorism squad chief, Rakesh Maria. Within 30 minutes, the in-charge of Juhu police station came to my residence, took my complaint and said I have been given police protection, " Aktar said.
The popular Bollywood lyricist said he had earlier received sms threats, but had ignored.
"I got different kinds of responses. While on one hand people had reservations about my stance, on the other I was applauded for my comments. You can voice your opinion but can't threaten anyone, " Akhtar told IBN7.