Pharmacists say they are paying as much as A$12 or more for the tests wholesale in some instances, as demand soared off the back of massive orders from state and federal governments in January.
The new scheme commenced on Monday with widespread complaints that pharmacies didn't have any stock when pensioners and concession cardholders asked for their "free" tests.
"The Government is reimbursing pharmacists A$10 for each test given out. However, at the moment many tests are costing more than A$10 wholesale,'' Pharmacy Guild of Australia president Trent Twomey said.
"The reimbursed price set by the Government has clearly been calculated on the whole cost of the tests around early December; the programme has built in reviews."
There is hope that supply chains will improve in coming weeks, which means retailers expect the unit cost at wholesale level to ease.
In the meantime, the per-unit cost of RATs has soared, which means the offer of a A$10 rebate is not always even covering pharmacists' costs and won't be paid to small businesses until the end of February.
"If the Government wants to improve accessibility they can improve the time frame for reimbursing pharmacies.
"The situation at present is that the Government will not be making the first payments until the end of February, which is more than four weeks away.
"Our community pharmacies across Australia are typically small businesses. Many small pharmacies can't afford to wait this long,'' Twomey said.
Pharmacists are also calling on the Federal Government to urgently provide more RATs as well as adequate personal protective equipment (PPE) for pharmacy staff.
Professional Pharmacists Australia (PPA) chief executive Jill McCabe said that pharmacists, who are trying to urgently roll out the booster and children's vaccination programme and also provide RATs to the community were at breaking point due to dire shortages of these vital items.
"Australia's community pharmacists can't do their job properly or safely without sufficient supplies of rapid antigen tests and personal protective clothing,'' she said.
Dr Geoff March, president of PPA, said the rollout was "reckless and negligent".
"The Federal Government's announcement that RATs would be freely available for six million pensioners and concession cardholders, without providing adequate logistical support to ensure pharmacies had access to these tests, was reckless and negligent.
"The Federal Government's announcement relied on pharmacies sourcing the RATs themselves, but a recent survey found that over 93 per cent of pharmacists have reported major difficulties accessing any supplies at all," said March.
"The shortages are taking a major toll on pharmacists themselves, with more than 75 per cent of pharmacists also reporting that the shortage of RATs had a 'significant' or 'extreme' impact on their ability to do their work.
"Yet again the Federal Government has failed to adequately plan and organise the supply of essential equipment to prevent the spread of the highly transmissible Omicron variant of Covid-19."
While the Federal Government has now advised it will provide temporary additional access to PPE from the National Medical Stockpile, only pharmacists administering the vaccine in community pharmacies will be eligible for this PPE and at the same time there are serious supply shortages.
"Pharmacists are working hard to roll out vaccination boosters and children's vaccination before the return to school, but can't do their jobs properly and safely without access to adequate PPE."
