In an interview with Buddhist/Atheist Dr. Khalid Sohail, Pervez Hoodbhoy acknowledges that he is a munafiq and says that his guru Eqbal Ahmad was one too and did not believe in the existence of God or in the Quran or the Angels or the Day of Judgement right upto the time of his death (May Allah protect us all from such a state):
Sohail: Your book, your articles and speeches make you appear as a Muslim scholar, Muslim scientist. Why do you not leave the religious podium and speak completely on secular terms?
Pervez: Well, that is a very vexing question. I think if you want to have any degree of credibility with people whose destiny you want to change, then you cannot say, “I am not one of you”. The reality is I was born a Muslim. I was for a while a very strongly practicing Muslim. All of us were brought up in a Muslim tradition. We cannot completely cut ourselves off from our roots. Let me tell you a story about Iqbal Ahmed. When he was dying, Raza Qazim’ s wife, who adored him, stood outside the room and read Quran for hours. When I informed Iqbal Ahmed. He invited her in and asked her to sit down. She was reading Quran even when inside. At one point I scribbled a note asking Iqbal Ahmed if I could request her to stop. He shook his finger, asking me not to do that. Later on when she left, I asked him, ‘Why did you tolerate this? You are not a Muslim’. “Of course I am,” he said. “No, you are not,” I insisted. “You don’t believe in Allah, the Quran, angels or the Day of Judgment”. “Yes, I am,” he still insisted. “I was born a Muslim and I will always remain that”. Although he never made any supplications to God, never asked for forgiveness, yet to the very end, he felt he was rooted in the culture he had lived in. I think it is a dilemma we all have. Though we may not believe in it, yet we were born in something and that something stamps us forever. So we are Secular Muslims.
The whole interview may be read here