He said they were there in solidarity with the families who had lost loved ones in the quake five years ago and to reflect on that disaster.
"I think it detracted from a solemn occasion, a fairly emotional service."
He said the substance looked like "a sludgy, stewy sort of mix."
It comes after Steven Joyce had a novelty fake squeaky dildo thrown at him at Waitangi on February 5, but the woman who threw it was not charged.
Mr Brownlee told Newstalk ZB a man had tipped a 2 litre ice cream container full of "pretty mucky stuff over my head".
He did not want to speculate on what was in the container, but it "didn't smell too good."
He said it had taken him by surprise.
"It was just a guy who just walked up at the end of the Memorial service and said' this is for you'."
A video of the aftermath of the incident on Mediaworks shows Mr Brownlee with his hair covered in brown sludge and smears of it on his face, glasses and down his front.
A man offers Mr Brownlee a handkerchief which he declines.
Mr Little can then then be seen patting Mr Brownlee on the back and appears to check he is alright.
A spokesperson for the Prime Minister said the memorial service was the time to remember those who lost their lives in the earthquake.
"While everyone has the right to protest, it's disappointing someone chose an occasion such as this to target a government representative in such a way. Our MPs work incredibly hard for their communities and it is unacceptable for anyone to be treated in this way."