Mr Hunt said the clinics would take "all comers" and distribute more than 1000 jabs each week.
More than 1000 general practices will join Australia's vaccination program from next week despite doctors' concerns they're short on doses. This will increase to 4000 clinics by the end of April as part of the rollout's next phase.
Mr Hunt conceded smaller general practices would need to focus on their own patients first before expanding to others.
"But the Commonwealth vaccination clinics that are coming online today will take all patients," he told ABC radio on Thursday.
"And with over 100 around the country, that's a very important addition. And they'll have, on average, close to a thousand vaccines a week and so that expands the capacity very significantly."
Australia's medicines regulator says there are no specific problems around either of the two COVID-19 vaccines, as GPs gear up for the next phase of the rollout.
The Therapeutic Goods Administration says it has received 19 reports of anaphylaxis - a form of allergic reaction - nationally, 14 of which followed the Pfizer vaccine and five followed the AstraZeneca vaccine.
As of March 15, the TGA had not received any reports of blood clots following the use of the AstraZeneca vaccine, which at least 17 countries are currently investigating while suspending or delaying the vaccine's use.
"We certainly don't believe there is any specific problem around either AstraZeneca or Pfizer COVID vaccines," the TGA's Professor John Skerritt said.
So far 204,000 Australians have been vaccinated, including 45,000 in aged care.
The next phase is set to begin on March 22, targeting people aged over 70, emergency workers and a range of other vulnerable groups.
Almost 12 million people had been vaccinated with the AstraZeneca jab in the UK without any evidence of blood clots. Allergic reactions had been extremely rare, with no cause for concern for people with no history of anaphylaxis.
The TGA has examined four cases of anaphylaxis in Queensland which related to vaccines from a single batch.
"TGA testing of the batch prior to release confirmed that it was compliant with all requirements.
"This particular batch of AstraZeneca vaccine has been used extensively across the country with only one other suspected case of anaphylaxis across the entire nation."
Professor Skerritt said the regulator had expected some allergic reactions with the numbers so far in line with the global experience.
The European Medicines Authority is adamant the AstraZeneca jab is safe, saying blood clot detections broadly mirrored rates in the general population.
Meanwhile, Labor is pressuring the government over missing its own vaccination targets and the failure of booking systems for general practice vaccinations.
Australia's doctors say the federal government shouldn't give unrealistic expectations around the COVID-19 vaccine rollout after GPs were inundated with calls from patients.
The Royal Australian College of General Practitioners has urged for calm amongst patients, pleading with them not to take their frustrations out on health workers.
There have been widespread reports of GP clinics being overwhelmed by calls from "impatient" people trying to book their vaccination appointment.
RACGP President Dr Karen Price said Wednesday was "a very difficult day" for surgeries, partly because of deficiencies in the federal Health Department's online booking system.
"It is clear from the phone calls being made to general practice that the government .. needs to better communicate with the community on the vaccine rollout process, and not build unrealistic expectations, particularly at this early stage," Dr Price said.
Some patients behaved "in a disrespectful and aggressive manner" towards administrative staff answering the phones.
"I plead with all people to please be respectful when speaking to receptionists and administrative staff managing this huge volume of calls about vaccines on top of their day-to-day presentations," Dr Price said.
GPs also need assurances about the supply chain of doses well ahead of time in order to match the demand with supply, staffing and practice logistics, she added.