He said that the delegation represented "the right mix" of New Zealanders and he did not feel there was a role for Mr Harawira to go to South Africa.
"This is a guy who has barely turned up to Parliament in 2013... He has spent a hell of a lot of 2013 doing anything other than actually taking his place in Parliament.
"He has to stand up to his own constituents, but I for one don't support what he's done."
A spokeswoman for Mr Harawira said that he attended a memorial service for Mandela in Soweto and also performed a haka at Mandela's house.
The Mana leader later paid his respects in Pretoria, where Mandela's body lay in state.
Mr Harawira's wife Hilda also travelled with him, and Mr Harawira was asked this morning if the taxpayer paid for her flight.
Newstalk ZB reported that he reacted angrily to the question, and he pointed to the $100,000 cost of sending the official New Zealand delegation.
Mr Harawira's office said that her trip was funded by private donors who wanted anti-apartheid protestors to attend the service.
Mr Harawira led protests against the Springbok tour of New Zealand in 1981 and wanted a protestor to be part of the group.
Mr Key defended the choice of New Zealand delegates, saying that he was under pressure to take a small number of people.
"I can't be sure but I'm pretty sure the Australian delegation was two. We took five and within half an hour of beginning they were still telling us we had to choose two to go to the actual memorial service."
He said anti-apartheid protestor John Minto - who many felt should have gone to South Africa - would "have his place in history".
The New Zealand delegation included Mr Key, Labour leader David Cunliffe, Maori Affairs Minister Pita Sharples, former prime minister Jim Bolger, and former foreign affairs minister Sir Don McKinnon.