It issued a "strike" under its three-strike policy, the last of which means permanent removal.
YouTube did not point to specific items but said it opposed material that "could cause real-world harm".
The TV channel's digital editor said the decision was a disturbing attack on the ability to think freely.
Sky News Australia is owned by a subsidiary of Rupert Murdoch's News Corp and has 1.85 million YouTube subscribers. The ban could affect its revenue stream from Google.
A YouTube statement said it had "clear and established Covid-19 medical misinformation policies based on local and global health authority guidance".
A spokesperson told the Guardian it "did not allow content that denies the existence of Covid-19" or which encouraged people "to use hydroxychloroquine or ivermectin to treat or prevent the virus". Neither has been proven to be effective against Covid.
The videos in question "did not provide sufficient countervailing context", the spokesperson said.
Sky News Australia said it had found old videos that did not comply with YouTube's policies and took its "commitment to meeting editorial and community expectations seriously".
But it denied any of its hosts had ever denied the existence of Covid-19.
Millions of Australians are currently in lockdown to prevent the spread of the contagious Delta variant, while fewer than 15% of the population are fully vaccinated.
Comments by veteran Sky presenter Alan Jones have triggered debate in Australia.
In one 12 July broadcast with MP Craig Kelly, both men claimed Delta was not as dangerous as the original and vaccines would not help.
The Sky News website issued an apology.
Sydney radio host Ray Hadley said Jones's performances had "allowed conspiracy theorists, anti-vaxers... to gain support from a minority who think the virus is nothing more than a dose of flu".
Australia's Daily Telegraph last week ended the column Jones wrote for it.
In an article on the Sky News Australia website, digital editor Jack Houghton said that if conversation about Australia's Covid-19 policies were stifled "our political leaders will be free to act with immunity, without justification and lacking any sufficient scrutiny from the public".
YouTube has issued dozens of bans over the past two years, several over Covid but most for hate speech.