Greg Hunt said the milestone was expected to be reached about 1pm on Thursday somewhere in Australia.
"About 1pm, in a country general practice, an Indigenous medical clinic, in a suburban pharmacy, someone will be the Australian who takes us over 90 per cent," Mr Hunt told reporters in Melbourne.
"We're at 81.9 per cent second doses, or almost 17 million people around the country who have had second doses, so that's a huge achievement."
It comes after Queensland on Wednesday became the last jurisdiction to cross the 80 per cent mark for first doses.
Mr Hunt said booster shot rates have already surpassed 200,000 doses after the top-up dose was approved for use in the general public late last month.
Medical regulators are now considering data from Pfizer to approve a vaccine for children aged five to 11.
The Therapeutic Goods Administration on Wednesday also granted a provisional determination for Moderna to submit its vaccine data for children aged six to 11-years-old.
Mr Hunt said Australia would get vaccines for children shortly, but careful consideration was needed from regulators.
"We're confident that this will be successful, but we're committed to making sure that that focus on safety is absolute," Mr Hunt said.
"(Regulators) will work to make sure that there are no corners cut in ensuring the safety and protection of our children."
The Pfizer vaccine has been approved for use in five to 11-year-olds in the US, following data from a trial in several thousand children.
Mr Hunt said Australia was watching the broader rollout of the vaccine to American children to get real-time data on its effectiveness and safety before a final decision on approval was made.
A decision is expected to be made before Christmas.
On Thursday, NSW reported 261 new local cases and one death while Victoria reported 1313 new infections and four fatalities.
As vaccine rates continue to climb, Prime Minister Scott Morrison has insisted he did not want to see anti-vaxxers demonised for refusing to get the jab.
Speaking on the Seven Network, Mr Morrison said he respected a person's right to choose, should they not want to get the vaccine.
"We live in a country where we are not going to go around demonising those who want to make their own choices," he said.
"Of course we want people to get vaccinated but we are not going to take that heavy-handed approach."
The comments were made after former NSW premier Bob Carr on Twitter called for anti-vaxxers to be stripped of their Medicare reimbursements, should they later contract the virus and be treated in hospital.