Some doctors "just thought it was wrong" and were worried about being labelled "Doctor Dope", he said.
"All I'm saying is that these decisions need to be based on the best interests of the patients, not the prejudices of the doctors. I'd like to see a more evidence-based and sound approach."
New Zealand Medical Association chairman Stephen Childs said Dunne appeared to be confusing untested or unknown cannabis products with pharmaceutical-grade cannabis products.
Childs said he would be "extremely surprised" if any doctor was declining applications to use proven, tested medical cannabis such as Sativex, a mouth spray used to treat multiple sclerosis.
Doctors would be "prudent" to be more sceptical of applications for non-pharmaceutical grade cannabis or lesser-known products, he said.
Dunne announced earlier today that he would be removing one barrier to accessing medical cannabis in New Zealand - the overly bureaucratic approval process.
As of today, it will be up to the Ministry of Health to approve patients' applications for the drug. That responsibility has previously been held by the minister.
Some cannabis law reformists wanted the Government to go further by delegating the role to specialists or GPs. But Dunne said that approach had not been successful in the United Kingdom.
"What happens there is the whole liability rests then on the medical practitioners who are entirely conservative as a consequence and don't prescribe anything.
"I don't think that's the outcome we want here."
As part of the policy changes announced today, Dunne also planned to create a list of internationally available, pharmaceutical-grade cannabis-based products.
The list would be used to guide doctors on the products which had no risk associated with their use, Dunne said.
Green Party health spokeswoman Julie Anne Genter said the new policy was a positive, but small step.
It did not address other barriers to medical cannabis for people who were sick or dying, such as the cost of the products. Sativex, the only product which has been approved in New Zealand, costs around $1300 a month.
EASIER ACCESS
Dunne said he told the Director-General of Health last week specialists seeking access to non-pharmaceutical, cannabis-based products would no longer need ministerial approval from today.
"Approval for pharmaceutical-grade cannabis products was similarly delegated some years ago," he said in a statement.
"As I stated in my delegation letter to the director-general, when applications first began to be received it was my view that the final decision appropriately lay at ministerial level, rather than exposing officials to risk, given the complicated and contentious nature of the issue - that is to say the buck stopped with me."
He said he had approved every application that has come before him within a matter of minutes.
"Since the first application was approved, guidelines have been developed, consulted on and simplified to allow specialists who are interested in accessing such products for their patients a clear, straightforward and unobstructed pathway to acquiring the appropriate products.
"I am satisfied that with the development of these guidelines, and with a number of successful applications having been subsequently completed, any risk associated with the early processes has largely abated and I have confidence in the Ministry of Health to handle the process in its entirety from now on."
The Government has come under pressure to relax the rules around medical cannabis after several high-profile cases drew national attention to the issue.
Former trade union boss Helen Kelly campaigned to be able to use cannabis legally for pain relief before her death in October.
And Rose Renton, mother of the first person to get approval to use medicinal cannabis in New Zealand, presented a 17,000-signature petition in favour of legalisation to Parliament late last year.
Renton's son, Alex, was given approval to use medicinal cannabis to treat seizures before his death last July.
