A Baptist church pastor charged with public nuisance offences after allegedly confronting Muslims at two Brisbane mosques this week, has had his visa cancelled.

Home Affairs Minister Peter Dutton reviewed the case and on Friday the Australian Border Force decided to cancel 31-year-old Logan Robertson's visa and prepare to send him back to New Zealand.

Pastor Logan Robertson from the Pillar Baptist Church in Ipswich. Credit:Facebook

Mr Dutton said the New Zealand national was taken into custody by Australian Border Force officers on Friday evening and was placed in immigration detention.

"My message is clear - if people come to this country they need to abide by the conditions of their visas," Mr Dutton said on Saturday.