The Medical Association (NZMA) says it did not consult with members before taking its stance opposing cannabis legalisation.
It confirmed what doctors have been telling RNZ, including members of the association's board, that the NZMA stance is not necessarily that of its members.
Senior figures at the association have since asked if members could be sent a rapid survey to clarify what the NZMA position should be.
They are concerned that the association is not representing the views of its members, and may need to clarify its position.
But the association chair, Dr Kate Baddock, said she has not received that request, and it is too late anyway.
She said the NZMA position is clear.
"Our position on cannabis has been around the harms of cannabis," Dr Baddock said.
"It's been there since 2012. It's been reiterated a few times over that time, and this is a board and organisational position - it's got nothing to do with me personally."
Doctors RNZ has talked to say the NZMA is misrepresenting their position on the referendum, and are critical of the fact they were not actually asked for their opinion.
This came after the NZMA told RNZ there was a robust process in place before announcing its position on the cannabis referendum.
Doctors also say the NZMA view is outdated, given it is based on advice first presented in 2012.
Dr Baddock admitted the NZMA has not looked at the overall impact of legalisation, and the actual proposed legislation itself does not appear to have been considered.
And she said the association's view does not consider doctors' individual thoughts.
"It's not like, do you like or not like the idea of recreational cannabis," she said.
"It's stating what the evidence shows, and on the basis of that whether in fact there are concerns that could legitimately be held about a certain process taking place."
Asked if the association would canvas members, as has been suggested by senior members of the NZMA, Dr Baddock rejected the idea.
"It would be a little late now since voting has begun."
And why were doctors not consulted before an organisational stance was taken?
"I just explained how policy is made, and that all comments with respect to the legalisation of recreational cannabis have been based on our mission statement."
Dr Baddock said the NZMA "didn't do anything" to further inform its position when the referendum was announced.
Last week, one doctor quit the association and others spoke out in support of the referendum because they said the NZMA stance was too narrow, and not fully formed.
Since then many more doctors have come forward, outlining their disappointment with the association's stance.