"The EC has been absolutely clear in their public and private statements that no further doses of (the AstraZeneca vaccine) are to be released until they have had their own orders fulfilled", Canberra said.
Morrison said he was also still awaiting an European Union response to an urgent request for one million of Australia's AstraZeneca doses to be diverted to neighbouring Papua New Guinea, which is facing a worrying Covid-19 surge.
However the EU has since denied responsibility, with the chief spokesman for the European Commission telling a press conference there had been no "new decision to block vaccine exports to Australia".
"There were over three million doses from overseas that never came", Mr Morrison said.
"We haven't given up hope but we've stopped counting them in our expected supplies", the source said.
His government, which received global praise for successfully containing Australia's coronavirus outbreak, has fallen far behind its vaccine rollout schedule.
Australia said on Wednesday the European Union asked it to withdraw export permit applications for AstraZeneca PLC's COVID-19 vaccine, ratcheting up its dispute with Europe over access to pre-purchased inoculations.
AstraZeneca did not immediately reply to a request for comment today.
She declined to say whether shipment requests to Australia were under review. But the Prime Minister is urging Australians not to focus on the "dust" being kicked up by critics of the program. "Those vaccines were not supplied to Australia", Morrison told reporters in Canberra.
"3.1 million vaccines didn't arrive in Australia - that's just a simple fact", he said.
But the latest supply blockages leave Australia struggling to step up the pace of its vaccination drive, which started much later than some other countries due to low case numbers.
Australia has recorded just 909 COVID-19 deaths since the pandemic began, a small number compared to most nations.
Its vaccine programme is now running well behind schedule, with only about 670,000 people inoculated against an initial target of 4 million by end-March.
Australia's prime minister on Wednesday (7 April) blamed restricted vaccine supply from Europe for his country's halting coronavirus inoculation efforts, as he faced down growing public frustration over the sluggish rollout.