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Immigration Minister David Coleman released a statement on Saturday after backflipping on a decision to grant Mr Yiannopoulos a visa into the country.
"Milo Yiannopoulos will not be allowed to enter Australia for his proposed tour this year," Mr Coleman said, after having granted him a visa a week ago.
"Mr Yiannopoulos' comments on social media regarding the Christchurch terror attack are appalling and foment hatred and division.
"The terrorist attack in Christchurch was carried out on Muslims peacefully practising their religion. It was an act of pure evil."
The government had agreed to the visa after conservative MPs had put pressure on Mr Coleman to override the Department of Home Affairs' advice to ban Mr Yiannopoulos.
"I'm banned from Australia, again, after a statement in which I said I abhor political violence," Mr Yiannopoulos said on social media after the announcement on Saturday.
Mr Yiannopoulos had described Islam as a "barbaric, alien" religious culture on social media overnight after the terror incident, prompting the government's change of heart.
Labor MP Tony Burke took to Twitter to praise the decision to ban the speaker.
"Milo banned. Good. His overnight comments weren't that different from how he has always behaved. There was already enough evidence to ban him which is why the department had already recommended he be banned. The Australian tours for the world's hate speakers must stop," he urged.
The speaking tour had previously been given the green light despite Mr Yiannopoulos owing Victoria Police $50,000 to cover policing at a Melbourne event in December, 2017, during which up to 500 left-wing protesters clashed with about 50 right-wing activists.