A controversial kiwi pastor has been arrested for allegedly abusing people at two Brisbane mosques.

Ali Kadri, head of the Islamic Council in Queensland, says on Wednesday afternoon Logan Robertson went to the Kuraby mosque with the intention to film.

After being denied entry, he harassed two 15-year-old boys and a 65-year-old man.

The Westcity Bible Baptist Pastor's next target was the Darra mosque.

This is where he also abused Kadri.

"[Robertson] started saying that... you have a cult of a religion, you are a terrorist, this [mosque] should be burnt to the ground, your Quran should be burnt to ground. He started throwing profanities at Prophet Muhammad."

Kadri says Robertson's visa has been cancelled and he will be sent back to New Zealand.

Australia's immigration minister Peter Dutton told reporters that people who came into the country needed to abide by the conditions of their visas.

"We have a wonderful tradition in our country of freedom of speech, but we're not going to tolerate people going to a place of worship and harassing others."

Robertson has previously attracted attention here in the past, with things he's said about and to gay people.

Last year, he made headlines after calling for homosexuals to be shot. He agreed his comments were hate speech, but was unapologetic.