The Australian Medical Association says its members are already reluctant to prescribe the drug.
But health advocates argue there is clear evidence of its therapeutic qualities.
The bill passed by the Senate removes restrictions placed on doctors treating terminally ill patients with medicinal cannabis produced overseas.
Under changes imposed by the Federal Government last year, they had been forced to apply to the Therapeutic Goods Administration.
Now medicos will only have to notify the Administration of their intention to do so.
Greens leader Richard Di Natale put the motion in the Senate to reverse the changes and allow faster cannabis treatment access for patients.
"That is going to improve their quality of life. We are talking about people who may have a brain tumour or stomach cancer. They are on chemotherapy drugs that cause people to experience nausea and vomiting, sometimes as a result of that people lose weight, their quality of life deteriorates. Medicinal cannabis is a proven treatment for this."
Medicinal cannabis proponents say the current system slowed down access for patients.
But the Australian Medical Association's President, Dr Michael Gannon, has told Sky News, doctors are already reluctant to prescribe the drug.
"This is no different to any other new drug, new technology, new operation. We want to be assured of the safety, assured of the effectiveness. So, you've already got a situation where doctors are querying how effective medicinal cannabis is. If you in any way put doubt in their minds about the safety, you're simply not going to see it prescribed by many doctors."
The Greens' motion passed the Senate after winning support from Labor, One Nation and other minor party senators.
But the Coalition opposed the move.
Health Minister Greg Hunt says the new law will open the floodgates to large quantities of cannabis coming into Australia that could be diverted by criminals.
He warns lives could be put at risk.
"Removing the safeguards could potentially allow in dangerous drugs that could take lives. That advice was given to Senate Estimates by the head of the TGA, Professor John Skerritt. It could also allow unregistered drugs to come in in quantities that could be used for diversion. Reckless and irresponsible. It's one thing for the crossbench to do this but it's completely another thing for an alternative government and an alternative prime minister to specifically sponsor unsafe drugs in unregulated quantities that could be diverted for criminal purposes."
But Richard di Natale says the minister's claims are alarmist.
"It's nonsense. It's utter nonsense. If we accept that medicinal cannabis is a treatment that's effective for people who are suffering and the evidence is very clear that that's exactly what it does, then why would we say that you can get access to other medicines from overseas that aren't available here in Australia but not medicinal cannabis. No, what we've seen is a government that has been dragged kicking and screaming to reform in this area."
The Health Minister says he won't simply accept the Senate vote, and is seeking advice from the Therapeutic Goods Administration about the possiblity of imposing new restrictions.
