The 85% shortfall comes two days after Brisbane entered another snap lockdown to combat a small outbreak.
Last week the government said the vaccine rollout did not demand urgency given Australia's low infection rates.
The country has recorded 909 deaths and 29,300 cases since the pandemic began - far fewer than many other nations.
But sporadic outbreaks have led to six lockdowns in cities in recent months. Critics say situations like Brisbane's outbreak show why a quick vaccine programme is still needed.
Brisbane's two clusters have been linked to a nurse and a doctor who contracted the virus from a Covid ward at the same hospital.
It's unclear why those health workers had not yet been vaccinated, officials said.
Critics have accused the government of mishandling the rollout, which began on 22 February - later than in many countries.
Australia is administering the Pfizer and AstraZeneca vaccines and has a rate of 2.3 vaccines per 100 people.
On Tuesday, Chief Health Officer Paul Kelly reported that 597,000 doses had been given so far.
In January, Prime Minister Scott Morrison promised to have four million people inoculated with their first shot by March.
Earlier this month, the government conceded it wasn't on track and pushed the target back to April. It also abandoned a promise to have every Australian fully vaccinated by October.