Commission President Gillian Triggs told SBS the public response to the 'Racism. It stops with me' campaign has been "unprecedented" and largely positive.
"We've had at least 117,000 hits on the website with people checking to see what the anti-racism strategy is," she said.
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However, she added, the response was tainted by a number of comments that were racist "and worse".
"We found by yesterday afternoon while we have had a number of people leaving comments, a hundred of those have really been so unacceptable, racist and worse, that we really couldn't provide a launching pad for those people."
While the Commission's Facebook page was the prime target, comments were also turned off on a YouTube video promoting the campaign.
The backlash came just two days after AFL star Adam Goodes, who is an ambassador for the campaign, was the target of alleged racially-motivated verbal abuse during a match at the weekend.
Ms Triggs said that the number of reported incidents about online racism did appear to be growing.
"To the extent that we're a barometer for understanding what the numbers are, I think we can say that we're seeing a rise."
But, she warned, it can be difficult to tell whether the rise in reports were simply a measure of "greater awareness" highlighted by an uptake of tools such as mobile video.
It follows a report released today by the Victorian Human Rights Commission which found incidents of online racism are becoming "increasingly prevalent" across the state.
The research was based on interviews with community stakeholders as well as a public survey of 227 people.
Victorian Human Rights Commissioner Karen Toohey said the Victorian Commission has also been targeted in the past with offensive comments left on their anti-hate website.
"For an organisation like ours, those comments on our website would sort of, re-vilify people coming to our organisation," she said.
"Hiding the comments is not about hiding the issue but about ensuring a safe place for those who are already vulnerable."
