The two women, described by police as taking part in "unrelated" protests, were later charged with disorderly behavior.
One woman climbed atop a wall, bared her chest and shouted "shame, shame" as Charles walked toward the City Art Gallery doorway. The woman, exposed from the waist up, was grabbed by two uniformed police officers, arrested and marched from the scene as the prince was led into the building.
In an apparent protest against the monarchy, the woman had the message "Get your colonial shame off my breasts" scrawled across her chest and stomach.
Reporters said the prince appeared to look in the woman's direction and smile as he entered the gallery.
Earlier in another part of the Civic Square, a bare-chested woman carrying a small child was hauled away by plain-clothed police moments before the prince would have been confronted by her as he greeted a line of well-wishers.
The woman, Holly Emma-Goldman, was protesting alleged reports that the prince was offended by aboriginal women who performed at a function topless during his official visit in Australia.
Although the protesters claimed Prince Charles had criticized the aborigines, British media who had been in Australia said he had not taken any offense.
Emma-Goldman was dragged away shouting, "I just want to feed my baby."
"She was breastfeeding her son pretty much to make a political statement that it is OK to have your breasts showing," said Emma-Goldman's friend Lisa. "It's freedom-like — and it does seem quite a racist connotation that he made as well."
Charles did not appear to notice the woman, local media said.
Both women arrested were later freed on bail, police said.
"These people they'll never be happy. They always want to complain or moan about something. ... We're here to see the prince and we're happy he's here," said a spectator. "These people are really bringing us all down. I wish they'd bugger off (go away)."
In another apparently linked protest, five anti-monarchists stood atop a wall with banners reading "Death to the monarchy" and "Honor the treaty," a reference to British crown breaches of New Zealand's founding treaty with the indigenous Maori people.
A woman with a bullhorn chanted, "Shame on the British monarchy, shame for years of colonialism, shame for years of genocide."
The protesters shouted "parasites, parasites" as Charles walked through the city's Civic Square greeting some of the more than 600 people gathered to see him. The protests caused no disruption.
The prince was on the third day of a five-day royal visit to New Zealand, a former British colony that retains Britain's monarch as head of state.
A growing republican movement wants to end the link and replace the monarch with a New Zealander. Some monarchists also oppose Charles becoming the nation's future king.