After initially publicly rejecting the allegations, the university announced an independent review, which will be led by Sir Wira Gardiner and Hekia Parata.
It is also now understood the university has decided not to renew the contracts of faculty dean Professor Brendan Hokowhitu, nor Tuhiwai-Smith.
The university told the Herald it would not discuss individual employment matters, but Matamua, said their experiences were indicative of wider systemic issues.
"They are world-renowned professors. Linda Tuhiwai-Smith is one of the world's leading indigenous academics - I don't know what institution in the world not have her."
Matamua, of Tūhoe, said the allegations emerging were the "tip of the iceberg".
Due to the university's review, Matamua said he could not go into specific incidents of racism, but said it was not a "culturally safe environment".
"We feel marginalised, invisible. We operate in an environment of fear that we will lose our jobs if we speak out. I am not sure if this is a place I can be anymore. I don't feel this is a culturally safe space."
Matamua, who joined the university in 2011, said issues had got "significantly worse" over that time, and included attempts to scrap the faculty and subsume it into the Arts and Social Sciences Division.
"We don't feel respected and recognised for the work we do.
"For instance, per head of staff we are arguably the most successful faculty at the university, but that is not recognised.
"Our research is not highlighted, nor our awards and significant accolades."
There was "massive under-representation" of Māori across the university, he said.
There were no Māori dean leaders, apart from in his faculty, and just 7 per cent of professors out of over 100 at the university were Māori.
"This is a hugely important issue for us, on builds on momentum across the globe including Black Lives Matter, pushing against injustice and racism."
Matamua is well known for his work in helping to elevate the understanding of Matariki as an important and significant occasion for New Zealanders.
This week the Labour Party promised to make Matariki a public holiday from 2022 if re-elected.
In July he was awarded the Prime Minister's Science Communications Prize, worth $100,000, from the Royal Society of New Zealand.
For him to stay on at the University of Waikato, Matamua said there needed to be an admission from the university that there was an issue around racism, and to make changes in the way it operated towards Māori and Pasifika.
"I do love the institution in terms of the students, and this faculty, but many of us are really struggling."
The university has not provided responses to questions from the Herald.
Instead, a spokeswoman said in a statement they could not comment on individual employment matters.
She reiterated the university had commissioned an independent review into the recent public claims about racism and that, once completed, the findings of the review will be made public.
