It is alleged that the Quran supports a concept known as Taqqiyah or deception, where by a Muslim may conceal the true nature of his or her beliefs by outwardly declaring something contrary. They would supposedly do this until more favorable conditions allow them to pursue their true agenda. For example, given the current atmosphere of Islamophobia, a Muslim may allegedly declare that Islam teaches tolerance of non-Muslims and social freedoms but deceivingly plots otherwise.
It is first important to cover the early history of Islam and how the doctrine of Taqqiyah developed particularly among one sect of Muslims: Shias. Shia-Muslims account for approximately 20% of all Muslims.
The primary difference between Shias and non-Shias is that the former believe that Ali (Holy Prophet Muhammad’s (on whom be peace) younger cousin) was the rightful heir to the leadership of the Muslim community upon Holy Prophet Muhammad’s (on whom be peace) demise. Hence, they do not recognize the leadership (or Caliphate) of Abu Bakar, Umar and Uthman who preceded Ali. This belief poses a problem because it is difficult to explain why Ali did not refuse to accept the leadership of the first three Caliphs and, in fact, took bay’ah (pledge of allegiance) at their hands.
The Shia clergy claims that Ali was performing Taqiyyah—meaning that he was hiding his true beliefs to protect himself. To support their argument, Shias point to verse 40:29 of the Quran where a man from the family of Pharaoh secretly believed in Moses’s teachings but concealed it for fear of crossing Pharaoh.
Non-Shia Muslims believe that while there may have been disagreement over succession to Holy Prophet Muhammad (on whom be peace), the situation posed no grave risk to Ali. He reconciled with the outcome of succession and served honorably under the first three Caliphs before being elected the fourth Caliph. Thus, there was no need for him to conceal his beliefs. On the other hand, concealing one’s belief in a situation of grave danger at the hands of a cruel and murderous tyrant like Pharaoh (who opposed Moses) is understandable and not viewed as a moral wrong.
Moreover, these accounts and verses are taken out of context by anti-Islam activists and apologists to paint all Muslims as having the belief that deception is justified for the purpose of spreading Islam.
The Quran champions honesty and integrity, and unequivocally condemns deception and lying as is evident from the verses below under the section: Fundamental Teachings of Islam.