Mr Morrison later told Question Time he did not support Mr Kelly's views.
"It is true that views expressed by the member for Hughes do not align with my views, or the views of advice that has been provided to me by the Chief Medical Officer," he said.
Mr Morrison has faced increasing pressure from critics over his previous reluctance to call out Mr Kelly following months of him posting online about coronavirus treatments.
The posts have been blamed for undermining public support in official health advice.
Opposition Leader Anthony Albanese said Mr Morrison's response was overdue and labelled Mr Kelly's comments "dangerous".
"I welcome the belated statements of the prime minister in distancing himself from the comments of the member for Hughes," he told Parliament on Wednesday.
In their earlier meeting, Mr Morrison made it clear to Mr Kelly he could not support his actions and asked him to refrain from pushing views contrary to the accepted medical advice.
Mr Morrison informed Mr Kelly his actions were negatively impacting the government's vaccine strategy and that he should focus on constituents in his Sydney seat of Hughes.
Tanya Plibersek confronts Craig Kelly over conspiracy comments in Canberra
It's understood Mr Kelly has agreed to restrain his social media use.
"This morning I had a meeting with the prime minister," Mr Kelly said in a statement.
"The prime minister reinforced the importance of ensuring public confidence in the government's vaccine strategy. I agreed to support the government's vaccine rollout which has been endorsed by medical experts."
"I believe that the spread of misinformation can damage the success of our public health response during the pandemic," he added.
Ms Plibersek had earlier told Mr Kelly she was concerned about the “crazy conspiracy theories” he was spreading during their clash.
“My mum lives in your electorate and I don’t want her exposed to people who are not going to be vaccinated because of these crazy conspiracy theories you are spreading,” Ms Plibersek said.
“You are the one doing that because you are the one spreading misinformation," Mr Kelly replied.
Mr Kelly has denied spreading misleading information about unproven coronavirus treatments, saying he has merely posted health advice backed by “senior qualified medical experts”.
He said he is not an anti-vaxxer and would consult with his family doctor about making a decision on taking a coronavirus vaccine.
Public medical experts have warned against the spread of misinformation by government MPs, saying it would undermine trust in official health information and could hamper efforts to smother the virus.
They've also called it irresponsible that the government have previously resisted speaking out against Mr Kelly's actions.
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