Racist, abusive and threatening comments were left by members of the public 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 on some stories, the 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.
Journalist Leanne Dolby told the inquiry earlier on Monday she was on the job reporting when a homemade bomb was thrown into a crowd in January at a Perth Invasion Day rally.
Thousands of people were evacuated from Forrest Place in the city centre after an object containing volatile chemicals, nails and metal ball bearings was found.
The device did not detonate despite a fuse allegedly being lit, and the incident was later declared an act of terror - the first in Western Australia's history.
Ms Dolby said police did not view her as a journalist covering a story.
"(I was) just an Aboriginal woman with a camera," she said.
"A big six-foot police officer towered over me, intimidated me and ... laughed in my face.
"I left this terrorist attack with a level of fear and a distrust for police, and a fear that one day I will die at the hand of a racist while I am working."
Perth man Liam Hall has been charged with engaging in a terrorist act over the incident.
Police will allege the incident was a nationalist and racially motivated attack targeting First Nations people at the protest.
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