Slides from the module of Universiti Teknologi Malaysia (UTM) caused uproar after they were posted online.
The slides claimed that Hindus consider the dirt on the body as part of their religious practice to achieve nirvana.
After the issue was raised by Deputy Education Minister P Kamalanathan, the university said it would review the module.
"I have just spoken to the Vice Chancellor of UTM and he has acknowledged the mistake," Kamalanathan, an ethnic Indian, said in a Facebook post.
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Muslim-majority Malaysia's 28 million population include 60 per cent Malays who are all Muslims, 25 per cent ethnic Chinese mostly Christians and Buddhists and eight per cent ethnic Indians, a majority of whom are Hindus.
The Minister said slides from the UTM module portraying Hindus as "dirty" could have been designed to intentionally misrepresent the religion. Commenting further, he expressed his personal disappointment over the messages in the slides that were leaked online, triggering Hindu outrage.
The module also claimed that Islam had introduced civility to the lives of the Hindu community in India.
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.
The slides led to condemnation by the Malaysian Indian Progressive Association (MIPAS) which called for a retraction and apology from the university.
"MIPAS condemns completely, the actions of UTM for publishing and allowing such a module that contains negative elements in its educational course that carries elements of insult and harassment as well as demean the purity of the Hindu faith," MIPAS secretary-general S Barathidasan said.
A police report was lodged by the chairman of the Hindu Dharma Association of Malaysia in Sungai Petani district against UTM, and expects more police reports to be lodged, Barathidasan added.