He said protests throughout history had ensured Maori had influence, and was important "in opening doors.''
Asked about the Prime Minister's comments, Dr Sharples said he understood where the Prime Minister was coming from. "From his position, it can be sort of a hiccup.''
However, he said the ability to speak out was critical.
"I don't think anyone should be made to stop protesting. It's a legitimate way to say 'I'm not happy with something.' And I think that's a cornerstone of our society - to have the freedom to do that.''
Dr Sharples said he did not believe there was a risk of the Treaty settlement protest being damaged by small groups of protestors.
"But clearly we all know that there are people out there who push the negative all the time.''
Mr Key gave the speech about an hour after the Dawn Service, following which he had said it was a quiet Waitangi Day and he had expected a greater level of protest, given the water rights case in the Supreme Court.
"So I thought there would be quite a lot of conflict aimed at us, but that hasn't been the case at all.''
Labour leader David Shearer also criticised the comments, saying Mr Key should have delivered the words at Te Tii Marae - in front of the people they were aimed at, rather than at a breakfast in front of a predominantly friendly audience.
"He's saying it to get a political hit in just before he gets in the car and drives off.''
After his speech, Mr Key would not name the protestors he was referring to, suggesting media check their film footage to find out who he was talking about.
In 2009 Mr Key was shoved by the Popata brothers and was shouted down last year by a mix of Maori and union activists.