Doctors are concerned access to codeine - which is only available by prescription from today - has been cut off with no viable alternative.
Canberra emergency doctor David Caldicott said the use of medicinal marijuana was an obvious solution for pain relief, which he believes is safer and more effective.
But the territory's acting chief health officer said there was a good availability of alternative medicines, denying there would be an influx of people attending GPs or emergency departments.
Nationwide changes mean drugs containing codeine will only be available by prescription, a move that came in response to a rise in deaths at the hands of opioids.
Dr Caldicott said while codeine was not an ideal drug, there was no clear plan to provide alternatives for regular users of over-the-counter codeine.
"I don't expect the withdrawal of codeine from the market will be without its unintended consequences," he said
Dr Caldicott said Australia's treatment of pain has been largely under the influence of the pharmaceutical industry
He said US states that introduced medicinal cannabis for pain relief saw drops in the prescribing of opioids and their associated deaths and overdoses.
"Patients are taking themselves off the opioids and the benzos because they are getting the same effect from a product that is far safer," Dr Caldicott said.
He said the fentanyl crisis in the US - when people turned to the drug when other opioids became harder to access - provided some insight into what could happen when access to a drug was suddenly cut off
He said he was concerned that making access to codeine or other opiates harder, Australians will also find a way to replace their opiates.
Dr Caldicott said it was not clear what a treating doctor should do when presented with a patient wanting to access codeine.
"People say this is a great initiative, but I see it as the medical profession commencing its atonement for a tremendous error of over-prescribing," he said.
"But the pain is real and other alternatives have to be made available to address this issue.
"It's just a little bit bizarre the most obvious intervention we could make is medicinal cannabis, which pretty much every country across the world is doing, but we are still dithering with it."
Chronic Pain Australia president Coralie Wales said the change was just another barrier for people with chronic pain and added to the stigma they faced.
She said there were many people who suffered from conditions such as migraines, endometritis and period pain who relied on easy access to low-dose codeine to attend work and complete daily tasks.
"What they're just having a dream, they're imagining it works?" Dr Wales said.
Dr Wales said people had been stockpiling drugs and will get panicky as that stockpile comes to an end and concerned doctors - under pressure to prescribe less opioids - would not prescribe them anything if they attend.
She said she was concerned people would be forced to consider black market alternatives.
"Some patients are saying it's just going to go underground," Dr Wales said.
"It could spawn a whole other market which is just unseen.
"Some patients are saying they will take whatever's in their cupboard."
But acting ACT Chief Health Officer Dr Paul Dugdale denied GPs, hospitals or patients would be under pressure due to the changes.
He said there were better over the counter options to low-dose codeine, including paracetamol and ibuprofen, and urged regular users of over the counter codeine products to see their GPs to come up with a treatment plan.
"Low dose codeine has been widely used for pain relief. There is growing evidence that the harms arising from over‑the‑counter codeine use and misuse substantially outweigh the benefits," Dr Dugdale said.
Canberra pharmacist Ben Gilbert, from Capital Chemist University of Canberra, said there had been a wide range of responses from customers finding out about the changes.
"People who don't have easy access to a GP are a bit lost, so we've been trying to hook them up," he said.
He said most codeine products have been unavailable for a number of weeks or months after it ceased being manufactured and stock ran out.