Racist, abusive and threatening comments were left by people on National Indigenous Times platforms daily, managing director Reece Harley said.
"The lessons that people have taken from the referendum are that it's OK to be racist in Australia," he told a federal inquiry into racism in Australia on Monday.
"It's OK to not care about Aboriginal Australia. It's OK to say whatever you want."
Social media companies such as Facebook were making the situation worse.
Mr Harley said their business model was to maximise engagement and eyeballs to boost revenue.
"So there is a commercial embedded incentive for these social media giants to not just allow, but actually to encourage people to say whatever they want, because people will fight back," he said.
"Racism online is organised, and it is escalating. We see it first, and we deal with it daily."
He said the racist comments were greatest when the media outlet reported on Australia Day, Stolen Generations and Indigenous languages, or when a person was interviewed and they were fair-skinned.
"Commenters deny people's Aboriginality," Mr Harley said.
"They demand to know percentages. They mock their families and question their right to speak."
Mr Harley said for some stories, racism outnumbered all other kinds of comments in a thread.
He said the abuse was silencing Indigenous Australians.
"Racism is shrinking the space in which Aboriginal people are willing to speak publicly," he said.
Mr Harley said there was no financial incentive to treat Indigenous people well in mainstream media because they were not seen as consumers.
"They are viewed by mainstream media as just kind of part of that story of what's going wrong in the country," he said.
Former Liberal Indigenous affairs minister Ken Wyatt said Australia appeared "to have slid back to an era that reminds me of some three decades ago".
"Racism is not merely a social problem," he said.
"It is a governance problem, it is a public policy problem, it is a human rights problem and ultimately, it is a question of national leadership."
Mr Wyatt said the true measure of a nation was not whether it acknowledged injustice, but whether it possessed the courage to correct it.
"It's not about assigning collective guilt, nor is it about judging one generation for the actions of another," he said.
"It is about whether Australia is prepared to examine the evidence honestly and determine whether every Indigenous Australian is afforded the same dignity, opportunity and protection under the institutions that serve us well."
National Indigenous Times journalist Leanne Dolby told the inquiry there was a daily deluge of vile racist comments on the media outlet's social media pages.
"I'm flooded with comments that tell us that Aboriginal people deserve to die, that racial discrimination is justified," she said.
"As our technology advances, so do newer avenues of racial discrimination ... and it feels like I am fighting a losing battle."
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