Both have since been released on bail, and are due to appear in the Whanganui District Court on Wednesday.
Across the country, 19 people were arrested at various events, including six people in Tauranga and one in Taupō.
Whanganui District Police Area Commander Inspector Nigel Allan said that, overall, compliance with alert level 4 restrictions had been good.
"This is the first incident of this nature we've had this lockdown. We spoke to the organiser yesterday and again today in an attempt to discourage this happening.
"We've done our best to educate the public around this and, as I say, it resulted in two arrests."
Whanganui mayor Hamish McDouall said the protest was irresponsible in the midst of a pandemic.
"The fact that there were two of them - I mean that's 0.005 per cent of the Whanganui population," McDouall said.
"I'll also note - it's somewhat misdirected. The Whanganui District Council didn't impose a national lockdown."
"There are people who disagree with this, I've heard the word 'plandemic' over the last 18 months. Some people don't believe in science - the world is made up of a multitude of different people."
Police Commissioner Andrew Coster said police were focused on ensuring the public followed alert level 4 restrictions.
"While protest is a normal feature of a well-functioning democracy, Police have a low tolerance for anyone who deliberately ignores the restrictions in the current situation. Today's arrests reflect that."
"The alert level is in place to protect us all and we need everyone to do their part."
