The Human Rights Commission has weighed in on the case of a Dunedin boy rejected for an exchange trip to Japan because he is Muslim.

Sharif Steel, 15, had hoped to spend a year in Japan staying with a host family but his application was rejected due to his religious beliefs, Stuff reported earlier today.

After applying, Sharif received an email from the exchange organisation World Youth Services saying their Japanese counterparts had "a few questions about you being a Muslim."

Sharif was told the problem stemmed from the fact that he did not eat pork, because "basically every Japanese family eats pork."

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The boy offered to pick pork out of his meals, but the organisation's decision not accept his application remained the same, Stuff said.

Sharif's family later learned the real problem was his application coincided with the capture and beheading of two Japanese nationals by Islamic State.

Richard Ellis, of World Youth Services, said the challenge was nothing to do with the boy.

"The fact was they were unable to find a Japanese family to host a Muslim."

Sharif told Stuff he had blamed himself for not being accepted, and was even more upset when he learned the real reason behind the decision.

Sharif's mother, Azizah, said the decision made her feel sick.

"I told him don't you ever feel ashamed that you are Muslim."

The Human Rights Commission encouraged the New Zealand student exchange organisation to contact their Japanese counterparts and work towards resolving an incident.

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"We've been in touch with the organisers of this student exchange programme and encouraged them to engage with their counterparts in Japan to address the problems that have arisen," said Race Relations Commissioner Dame Susan Devoy.

"We also encouraged them to work with Sharif and his family to resolve this incident.

"Student exchanges are primarily about intercultural education and a key part of intercultural relations is to keep talking and to sort things out."

Religious discrimination in New Zealand is unlawful under the Human Rights Act.