The Johor Religious Council adviser and the Mufti of Perak both state that images of crosses, liquor brands and devils on football shirts are an insult to Allah and should not be worn by Muslims.
Manchester United is a hugely popular brand in the Muslim-majority country.
The club's summer tour last year included two games against a Malaysia XI played in front of capacity 40,000 crowds.
Other football shirts deemed unacceptable by the religious leaders include Brazil, Portugal, Serbia, Barcelona and Norway because their crests all carry images of a cross.
"There is no excuse for wearing such garments because it means, as a Muslim, you are idolising the symbol of another religion," Datuk Nooh Gadot, the Mufti of Johor, said.
"On this matter there is absolutely no compromise in the name of entertainment, fashion or even sports."
The Mufti of Perak, Tan Sri Harussani Zakaria, said that Muslims wearing such football shirts "leads to a path of sin" because displaying the symbol of another faith means the wearer is prioritising that faith over Islam.
In March, Manchester United signed a five-year sponsorship deal with communications group Telekom Malaysia, further raising their profile as the leading sports team in the country.
"Anyone who went on our tour of the Far East last summer knows the strength of feeling that Malaysians have for the club," David Gill, Manchester United chief executive, said.
The warnings about "sinful" red devil shirts have sparked furious reactions on the many Malaysian fan sites.
"Soon, they will suggest changing the arithmetic symbols such as "+" and "x", because these symbols are not halal," commented on computer on a fans' website.
Malaysia's reputation as a moderate and progressive Muslim nation has suffered this year after the firebombing of churches in January and the caning of three Muslim women for adultery in February.
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