It is estimated up to 3.5 per cent of them suffered horrific physical, sexual and mental abuse while in care.
The vast majority of children taken were Maori, Dame Susan told the UN committee.
"These state homes were the beginning of the mass incarceration of Maori New Zealanders in our state institutions. And it is still going on.
"The refusal by successive governments to investigate is not only wrong, it is immoral. This is not my New Zealand and I urged the UN to tell our Government to do the right thing."
Prime Minister Bill English has effectively ruled out setting up an independent inquiry into the claims. He considers it more important to make changes to child welfare services to prevent a repeat of the abuse.
However after the petition was delivered in July he softened his stance, saying he was willing to listen to what the victims had to say - but suggesting he was yet to be convinced of the merits of a large-scale inquiry.
Dame Susan is representing the Human Rights Commission before the UN Committee on the Elimination of Racial Discrimination (CERD), which monitors whether countries are complying with anti-discrimination laws.
"We live in one of the most peaceful and ethnically diverse nations on earth and yet racism happens in New Zealand," she told the committee.