Federal Health Minister Nicola Roxon is seeking advice from her department on how to fix problems that have resulted in thousands of health professionals being left unregistered and unable to practice.
Ms Roxon intervened after claims that doctors, physiotherapists and other health workers failed to gain medical registration under the new national scheme introduced in July.
The Health Practitioner Regulation Agency's chief executive, Martin Fletcher, concedes there have been "teething problems" and has promised to fast-track registrations.
"Since July 1, 2010, which is when the national scheme commenced, we have renewed the registration of more than 290,000 practitioners and we have also successfully registered more than 24,000 new health practitioners," he said.
But the Australian Medical Association says thousands of doctors have not yet been registered.
Some do not even know they are not registered and, as a result, they could be prosecuted for professional misconduct, cannot claim Medicare rebates nor can their patients.
But Mr Fletcher says they are advising doctors who have not re-registered as quickly as possible.
"If a health practitioner for some reason doesn't renew their registration on time, and they are meant to do it every year, what we've done is we obviously advise them of that," he said.
"And we have put in place a fast-track procedure where we can very quickly, once we get the application from the practitioner, get them back on to the register and we've waived any fee for that."
But Mr Fletcher says he cannot guarantee Medicare or private health insurance rebates for non-registered doctors and their patients.
"We don't administer the Medicare or private health insurance scheme. Our responsibility is to make sure people are appropriately registered," he said.
"And if they have failed to register, and sometimes people choose not to register again, [our job is] to make sure they know how they can quickly get themselves back onto the register so they can continue to practice.
"We are working very closely with Medicare and the federal health authorities to make sure the introduction of the national scheme is as smooth as it can be."
Some doctors are reported to have sought compensation from the Department of Finance so patients can get their Medicare rebates for treatment they would have missed out on while the doctors were unregistered.
Mr Fletcher has also defended the problems encountered so far.
"We've renewed hundreds of thousands of practitioners and registered tens of thousands of new health practitioners," he said.
"I think we have acknowledged there have been difficulties for people in contacting us, especially at very busy times and this is something we are very focused on fixing.
"From today, for example, we are extending the opening hours of our contact centre to make sure it is easier for people to get in touch with us, and we are providing more and more services everyday online so people can go onto our website and get the information and assistance they need."
Opposition health spokesman Peter Dutton says Ms Roxon needs to fix the problem quickly.
"This is an incredibly important issue for local communities, because if doctors and nurses who have the qualifications and have been practicing have now been stopped from practicing because of a bureaucratic muck-up, then it's a real outrage and it's a problem for communities," he said.