Among the deleted passages is the video for the British rock band's 1984 hit "I Want To Break Free", the publication reported.
The clip sees all of the band's members in drag, with Mercury vacuuming in a black miniskirt and a sleeveless pink turtleneck.
Another scene, in which Mercury tells his one-time fiancée Mary Austin that he is bisexual, was cut as well, the Malay Mail wrote.
In Malaysia, Bohemian Rhapsody has been given an 18 rating, while it's deemed PG-13 in the US and in the UK.
Discrimination against gay, lesbian, bisexual, and transgender people is "pervasive" in Malaysia, as previously noted by Human Rights Watch.
In September this year, two women aged 22 and 32 were caned in the country after attempting to have consensual sex with each other.
Disclaimer for watching #BohemianRhapsody in Malaysia: they cut out ALL the gay scenes thus leaving out HUGE PLOT HOLES.— MalayVines™ (@MalayVines) November 9, 2018
I watched it in both Singapore & Malaysia & I realise you won’t fully understand if you watch it in Malaysia. Recommend to watch someplace else!!
Some people have criticised the censorship of Bohemian Rhapsody on social media, saying the cuts make it hard to follow the film.
"Disclaimer for watching Bohemian Rhapsody in Malaysia: they cut out ALL the gay scenes thus leaving out HUGE PLOT HOLES," one person wrote.
"I watched it in both Singapore & Malaysia and I realise you won’t fully understand if you watch it in Malaysia. Recommend to watch someplace else!!"
In other parts of the world, the biopic, which stars Rami Malek as Mercury, has been accused of glossing over parts of the singer's life, such as his sexual orientation and his HIV diagnosis.
Despite mixed reviews, the biopic scored the second biggest box office opening for a music biopic following its release in October.
The film reached $72.5m (£56.4m) at the worldwide box office with an additional $50m (£38.9m) in the US, amounting to a global launch of $122.5m (£95m). As Forbes noted, it has since topped $100m (£77.8m) domestically.