YouTube owner Google, also giving evidence, said 23 Sky News videos have been deleted, among more than 5,000 items of Australian misinformation.
The barred material included the promotion of “cures” and the denial that COVID-19 is a pandemic.
Sky News Australia was suspended from YouTube for seven days in August for material that “could cause real-world harm”, under the platform’s three-strikes policy.
The media giant had issued an apology in July after broadcaster Alan Jones and then Liberal MP Craig Kelly dismissed vaccines and claimed the Delta variant was less dangerous than the first strain.
Mr Whittaker said host Cory Bernardi was spoken to about his private tweet that claimed “ivermectin will set you free”, which the former conservative senator subsequently deleted.
Former prime minister Kevin Rudd said Sky News and News Corp co-chair Lachlan Murdoch “have a case to answer” for vaccine hesitancy and the promotion of “quack medicine”.
Half a million Australians have petitioned parliament for a royal commission into the media giant.
Mr Rudd said it was “utterly spineless” of Mr Murdoch to decline to front the inquiry, given his level of control over the “raw meat” being served up by Sky News.
Mr Whittaker told the hearing it was in the public interest that the drugs ivermectin and hydroxychloroquine were discussed, particularly last year when there were no vaccines available.
“It’s a scientific debate that continues to this day,” he said.
Committee chair Senator Sarah Hanson-Young also grilled Google on the “COVID lies” she said Sky News had been spreading for more than a year, including on social media.
Google enforces its own COVID-19 misinformation code and says it has worked with health and media authorities in Australia and around the world.
“Where there are videos that, without further context, assert that those drugs [ivermectin and hydroxychloroquine] are effective we remove them because of the danger and medical harm that could be caused to users,” Google Australia spokeswoman Lucinda Longcroft said.
More than 5,000 “dangerous and misleading” videos traced to an Australian IP address were removed from YouTube between February 2020 and March 2021, including the Sky News Australia material.
Ms Longcroft said most of the Sky News items were removed due to their “violation” of the COVID-19 misinformation code and two for violations of political integrity rules.
“They have been permanently deleted,” she said.
Mr Whittaker said there were no public complaints about them, and no action has been taken by the media regulator, the Australian Communications and Media Authority.
He denied accusations that he had prevented news hosts from giving evidence at the hearing, saying it was their personal decision.