The New Zealand Medical Association is angry that the Pharmacy Council will allow pharmacies greater freedom to sell alternative products.
The Council previously had a code which required credible evidence of the efficacy of a product before it could be sold at pharmacies, but this is changing on March 12, Newsroom reports.
Under the new rule, pharmacists can sell products with no scientific evidence that they are effective, but must tell the customer that.
Homeopathy is a pseudo-science invented in the 1700s, and practitioners believe extremely diluted solutions often containing no active ingredients can help with various health issues.
Practitioners believe the more diluted the solution is, the more effective it is, and usually repeat the dilution process so many times that no molecules of any active ingredient remain.
Its effectiveness has been widely disproven by large-scale studies.
New Zealand Medical Association's Dr Kate Baddock, speaking this morning to TVNZ 1's Breakfast programme, said putting "alternative and complementary" products on the shelves next to scientifically-proven ones gave them an air of legitimacy.
"By putting them in a pharmacy, it lends them a legitimacy that they don't necessarily deserve," Dr Baddock said.
"The medicines which have got validity and scientific trials behind them, they are significantly regulated ... so yes, you do know what they'll do and you do know what they won't do and you actually know the side effects."
Chief Executive of the Pharmacy Council Michael Pead told Breakfast he is "excited" to change the code, saying it is "recognising the credibility of our pharmacists".
"We all need to realistic - complimentary alternative medicines exist across the board," Mr Pead said.
"Our pharmacists have always worked very closely with our patients ... they work closely in making sure that our patients make informed choices."
Mr Pead said the new code is aligned with the code in Australia, and that the previous guidance document for pharmacists, created in 2011, was "not enforceable".
"We work very closely with our pharmacists to ensure public safety," Mr Pead said.
"Our pharmacists are well trained, very credible, extremely safe and are doing exactly the same as what is expected of doctor."
Mr Pead emphasised that the Council is not there to regulate the medicines or products, but simply to regulate the pharmacists and how they practice.