The teacher revealed in a video posted to Facebook that his hat has been taken from his head by protesters and later burned, which he said was "kinda funny".
Photos show the flaming MAGA hat being held aloft by a female protester wearing a black bandana, before being stomped on.
He was among thousands of people to line central Auckland streets during Monday's protest, organised in the aftermath of the death of George Floyd at the hands of a white police officer in Minneapolis, US.
His decision to wear the pro-Trump hat sparked angry scenes among the protesters, who accused the teacher of being a "racist" and of antagonising the crowd.
Manukau Christian School is now fielding complaints from parents concerned about his behaviour.
Principal Pete Slaney has reportedly said the incident is being handled internally and that the school does not condone racism.
Bearing Donald Trump's 2016 campaign slogan, the MAGA hat has been used by Far Right movements in the United States.
National leader Todd Muller recently came under fire for showcasing his MAGA cap in an office cabinet, defending it as political memorabilia after many said it represented racial oppression.
Muller later said the hat would stay in its box and won't be unpacked as he moved to his new office.
The teacher said he and a friend, who was also wearing a MAGA hat, were "very lucky not to get jumped" at the march.
"I was attacked, I had my hat stolen from me. I was grabbed by the collar, pushed around."
The video ends with clips of the man's interactions with other protesters, many of whom are furious to see the MAGA cap at a march of solidarity against racism.
Dozens of people tell him to "take the hat off".
"Its antagonising because that hat stands for racism and you know it," one protester tells him.
"You're antagonising people."
Another protester, who reportedly attends the same church as the teacher, urges the man to remove his MAGA cap.