Higher Education Minister Idris Jusohhas handed over the case to the Universiti Technologie Malaysia's (UTM) disciplinary committee.
"We view the matter seriously because in a multi-racial country, we have to have tolerance and respect for one another," he was quoted as saying by state-run Bernama news agency.
The lecture materials, in the form of slides for UTM Tamadun Islam Tamadun Asia (Titas) subject had caused an uproar among the minority Hindu and Sikh communities here after the contents went viral recently.
The module also claimed that Islam had introduced civility to the lives of the Hindu community in India.
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Another slide aimed at teaching the origins of Sikhism claims that founder Guru Nanak had a poor understanding of Islam and had combined it with his surrounding Hindu lifestyle in forming the early foundation of the Sikh faith.
Muslim majority Malaysia's 28 million population consisted of 8 per cent ethnic Indians.
Idris said the university, as an institution with autonomy, is empowered to take action against the lecturer or lecturers responsible for producing the slides.
India had expressed concern over the "negative and incorrect" picture conveyed about Hinduism and Sikhism in the educational module.
"We are concerned at negative and incorrect picture being conveyed about Hinduism and Sikhism. Hinduism and Sikhism are two great religions which India has given birth to," theHigh Commission of India in Malaysia had said in a statement last week.