With supplies running short, bookings for first doses of the Pfizer vaccine through the state's COVID hotline have been halted for this week with appointment times to be progressively made available next week.

At the Ballarat Health Service's Community Vaccination Centre at the Mercure on Monday, patients were being advised to book their second dose in three weeks but when calling the state COVID hotline to book an appointment were told they must wait six weeks.

COVID hotline call takers said the delay was due to the effectiveness of the vaccine being better if given five to six weeks after the initial dose rather than the three weeks advised by health authorities and made no mention about supply shortages.

The Department of Health and Human Services confirmed that around 50,000 Victorians have booked in for their first Pfizer dose this week - this is the number of first doses which can be administered while also delivering second doses for tens of thousands of others.

Every first dose booking already in the system for this week will proceed.

DHHS said this week, vaccination centres would focus on administering second doses of the Pfizer vaccine to the large number of people who came forward to receive their first dose from three weeks prior when the expanded eligibility for people aged 40-49 began.

Mass vaccination centres in Melbourne which had been offering walk-in appointments for Pfizer vaccine also suspended their service on Monday.

In a tweet, chief health officer Brett Sutton reassured those waiting up to six weeks for their second Pfizer jab.

"Getting your second dose anytime between 3 and 6 weeks after first dose is fine. The higher range dosing interval at least equivalent for immunity, and possibly even better," he wrote.

DHHS said in a statement that Victoria followed the advice of Australia's technical and medical experts - ATAGI, which recommended second doses of the Pfizer vaccine three to six weeks following the first.

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"The vaccine booking hotline offers Victorians the ability to book a second dose within this window. We recommend all Victorians who have not yet booked their second dose to do so by calling 1800 675 398."

The recommended interval between two doses of Pfizer is at least 21 days, and it is recommended to complete the two-dose course within six weeks.

To date there have been 797,472 vaccine doses given at Victorian state-commissioned services and more than 1.7 million doses across state, general practice and Commonwealth programs in Victoria.

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