Mr Christensen's latest anti-vaccination remarks, which have been quickly condemned, were made during a podcast interview with American virologist Robert Malone, who has been banned from social media platforms for COVID-19 misinformation.
During a media conference on Wednesday, the prime minister urged parents not to listen to Mr Christensen's views.
"I think they're unwise views, I think they're dangerous views. I don't think parents should be listening to them," he said.
"I don't think anyone should be paying attention to him on this issue."
Mr Christensen, who is resigning from politics at the next election, has often made anti-vaccination remarks during the pandemic.
He previously in parliament likened COVID-19 restrictions to the regimes of dictators such as Adolf Hitler and Pol Pot.
His latest comments could see the Dawson MP removed from his position as chair of a parliamentary trade and investment committee, a role that earns him extra money on top of his backbencher salary.
However, Mr Morrison stopped short of calling for Mr Christensen to be expelled from the coalition party room.
"Australia is a free country, you can't go locking people up for what they say as Australians," he said.
"His views are not the government's views ... I can only encourage those to simply ignore him."
Mr Morrison has spoken to Deputy Prime Minister and Nationals leader Barnaby Joyce about Mr Christensen's comments.
Speaking to reporters in Brisbane, Mr Joyce said Mr Christensen's comments were not backed up by medical experts.
"It's quite obvious it's at odds with the position held by the appointed medical authorities on this very important issue, and that is something taken into account," he said.
"His comments are not backed up by medical workers in that field."
Labor health spokesman Mark Butler said the comments from Mr Christensen were outrageous and urged the government to pull him into line.
"This guy is not a fringe commentator. George Christensen is a menace to pubic health," he said.
"He's a danger to the public health of our children, no less, and there should be no place for him in the government party room."
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