Federal Labor is calling on the government to take the same hardline stance against their own MPs who have undermined the vaccine rollout that it did in its approach to Novak Djokovic's visa cancellation and deportation.

The world men's tennis number one left Australia yesterday after losing a final legal challenge to have his second visa cancellation overturned.

Immigration Minister Alex Hawke used his ministerial powers to cancel the 34-year-old's visa on health and good-order grounds.

In documents tendered to the Federal Court during Djokovic's last appeal, lawyers for the minister argued part of his decision was based on concerns he was an "icon for anti-vaccination groups".

Shadow Affairs Minister Kristina Keneally said if the government and Prime Minister Scott Morrison were concerned about those who opposed COVID-19 vaccination, then they should also pull into line government MPs who had questioned the need for vaccine mandates.

"Members of your own government out there in Australia, enticing anti-vaccination sentiment, undermining the vaccination rollout," she said.

"If you really care about supporting the vaccine rollout, if you really care about ensuring that kids get vaccinated … stand up today and … be clear, condemn [and] call out [government MPs] for their anti-vaccine sentiment because it is genuinely a risk to Australian public health."

Last year, five government senators — Matt Canavan, Alex Antic, Gerard Rennick, Sam McMahon and Concetta Fierravanti-Wells —crossed the floor to support a bill that was calling for an end to vaccine mandates.

In the lower house, controversial Queensland MP George Christensen has been outspoken against COVID-19 vaccination mandates and lockdowns.

Senators Rennick and Antic also threatened to withhold their votes unless the federal government stepped in to end the state-based mandates.

Senator Rennick posts prolifically on social media about vaccine "injury" claims, and his Facebook engagement surged last year in response to some of the posts.

Speaking on Nine radio, Mr Morrison said the Djokovic matter and government MPs' views were "two different issues".

"If you're an Australian, you're a citizen, you're a resident, you can be here and you can express your views," he said.

"This is about someone who sought to come to Australia and not comply with the entry rules at our border."

Treasurer Josh Frydenberg echoed the Prime Minister, saying the comparison between Djokovic and MPs could not be made.

"Well, firstly I don't share those views of my colleagues who are opposed to vaccinations," he said.

"Novak Djokovic is not an Australian citizen so he has different rights to an Australian citizen.

"You can't compare those two cases but I can certainly disagree with Novak Djokovic and also disagree with anyone in the parliament who doesn't support the vaccination program."