Members of a Muslim sect in Cardiff claim they are facing discrimination from other Muslims in the city.
Worshippers at the Ahmadiyya mosque in Canton said other Muslims had shunned them, with one claiming he was sacked from a restaurant and another that he was accosted for selling Islamic books.
The Muslim Council of Wales (MCW) said it "abhorred" any type of persecution.
The Equality and Human Rights Commission confirmed it had "received correspondence" about the matter.
In a written statement, the MCW said: "Sunni and Shia Muslims do not recognise Mirza Gulam Ahmad as the Messiah... whereas the Ahmadiyya do.
"This forms a theological schism, and one which the majority of Sunni and Shia scholars consider to mean that Ahmadiyyas have moved beyond mainstream Islam.
"We abhor strongly any persecution based on religion, race, gender, disability or sexual orientation and support the religious freedom of all, including the Ahmadiyya.
"This is a value that unites Muslims and faith groups across the globe."
Mubarik Bashir, who prays at the Ahmadi mosque, claimed he was fired from an Asian restaurant in the city because of his beliefs.
He said: "I went to work there for three weeks. [But I was told] the owner is not happy with me. They told me 'I think you're Ahmadi. My customers are not happy. Please leave this job'.
"I was very upset. After that I wasn't working for two or three months."
Another member of the community, Arshid Mahmood, said he had been verbally abused for selling Islamic books.
He said: "Two years ago we held a [religious] bookstall in Cardiff Bay. Three Arab Muslims came and said 'well done'... and took three or four books to distribute.
"After 10 or 15 minutes they came back and threw the books and said 'you are not Muslim. Why are you distributing these books?'
"They abused us and went."
Abdur Shakoor, who also worships at the Sanatorium Road mosque in Canton, said other Muslims had refused to greet him.
"I work in an Asian community… I try and say 'Salam Alaikum' to them and they won't answer it, they won't say 'Salam Alaikum' back to you or give you respect," he said.
Fiyaz Mughal, director of Faith Matters, which works to reduce religious conflict, said this kind of discrimination had "gone unchecked for too long".
"Imported thinking from Pakistan and elsewhere has seeped into the mindset of some orthodox Muslims in this country," he said.
"Unfortunately, there seems to be no room for pluralism."