Mr Canavan said Australia and the United Kingdom were now isolated in continuing on with the deployment of the AstraZenica vaccine.
"Given that we are in a country that does not face an imminent risk of coronavirus spread then surely the prudent approach here is to suspend our rollout and just take a look at the evidence that will emerge in coming months," Senator Canavan said.
"The evidence from all of these other countries' decisions indicates that there is a risk, and that has to be a relevant discussion for us."It's clearly time for us to suspend the rollout here in Australia if almost every European country is doing the same."
A small number of reports have emerged of people being vaccinated experiencing blood clot issues, though no conclusive evidence has yet linked it to the vaccine.
AstraZenica has insisted the vaccine is safe, and that it has analysed data from 17 million doses. The drug giant yesterday released a statement saying any occurrence of clotting was consistent with normal levels found among the general population.
Australia's Therapeutic Goods Administration (TGA) has approved the vaccine, but the US health has yet to clear it.
Earlier this morning, Treasurer Josh Frydenberg said the Federal Government is confident in the safety of the AstraZeneca vaccine and that expert medical advice maintained the jab was safe.
"The World Health Organisation and the European equivalent of the TGA have both confirmed the effectiveness of the AstraZeneca vaccine and have said they have no evidence of that causal link between the vaccine and blood clots," Mr Frydenberg told Today.
"In the United Kingdom they have successfully rolled out that vaccine, more than 12 million doses. They haven't seen that pattern or those trends in those people who have received it."
When asked by reporters if his views were alarmist and jeopardising the national vaccine rollout, Mr Canavan replied he did not believe the TGA was "infallible".
"This might well very prove to be a safe vaccine," he said.
"There's just not the imminent risk here in this country so why don't we pause and take a breath."
The Australian government has ordered more than 50 million doses of the AstraZenica vaccine, and it is the largest vaccine supply in the country.
Any pause of the vaccine would have a serious impact on government vaccination plans in 2021, and impact on travel, tourism and business.
Mr Canavan said he had raised his concerns with Health Minister Greg Hunt, but he was yet to receive a reply.
Former head of the Australian Medical Association Tony Bartone said moves in Europe to suspend the rollout were only precautionary, and that there was no concrete evidence the vaccine was unsafe.
He said the TGA was "one of the safest regulatory regimes in the world" and the agency was on top of all key data and evidence.
Dr Bartone said "there is no proof, no evidence" that the vaccine heightens risk of blood clotting.