The majority of British administrators adhere to the philosophy of logical positivism (later known as logical empiricism), referred as an understanding that emphasized on the use of the intellect as the main approach to obtain accurate scientific facts based on meticulous and systematic research methods. This philosophy rejects the proof of a fact from the source of revelation as it is considered not relevant in proving the history and has created a bigoted and queried views towards the Malay community in Malaya. This article focuses on the analysis of the British administrators’ views on the system of education in Malaya, which include religious and secular education, and to determine the influence of Islamic religious education on the community. The methods used were historiography, comparative method and content analysis. The study found that the British administrators had underestimated the contribution of Islamic education system in Malaya and considerered the failure of Malaya in achieving its high civilization was due to the adherence to Islam which was considered as irrelevant and outdated. Hence, to improve these weaknesses, Western education system was seen as an appropriate step to internalise secularism into the thinking of the Malays in Malaya.