Guild chief executive Annabel Young said the letter sent to GPs by the Otago and Southland district health boards was "flying in the face" of part of last year's national agreement between boards and the guild.
Otago board chairman Errol Millar, who came up with the idea of the letter, said that was Ms Young's interpretation and he would not want "bureaucracy to get in the road of common sense".
The letter is signed by Mr Millar, Southland board chairman Paul Menzies, Primary Health Organisation Transition Board chairman Conway Powell and South Link Health executive director Prof Murray Tilyard (who also chairs the transition board's clinical health services subcommittee).
Headed "Cost of Community Pharmaceuticals", it says it is a personal appeal to GPs to help the boards, which are under "tremendous financial pressure".
The boards were spending an average $261.94 per patient in this area, $7.24 above the national average.
This variance accounted for $2.071 million of the total spending on community medicines in the two provinces last financial year of almost $80 million.
The letter recognised good work done by South Link Health and the Best Practice Advocacy Centre on prescribing practice, as shown by the regions' better use of cheaper, equivalent generic brands. However, it added the boards "simply cannot afford our current and projected pharmaceutical costs".
The variation in pharmaceutical prescribing practice appeared to be beyond that which could be explained by the variation in individual patient need, although it was accepted some GPs would have a higher than average prescription cost due to their mix of patients.
The letter says if the boards cannot bring medicine spending into line with funding, there would be no alternative but to reduce some other much-needed service.
"Our plea to you is to please help us to ensure we retain our services to the community by exercising prescribing restraint where possible," the letter ended.
Mr Millar said he had received no feedback from GPs since the letter went out a week ago.
The board did not want doctors to cut corners to save money and the wording of the letter had been very careful, he said.
Boards chief executive Brian Rousseau said the letter was not saying GPs were not doing their job, just asking them to be aware of the financial situation when they were writing prescriptions.
Prof Tilyard said feedback to him from GPs had been positive. It was good to be reminded that prescribing was a key area of expenditure and of the need to minimise waste.
Ms Young said community pharmacies had agreed to accept no increase in the $5.30 dispensing fee in the new agreement which came into effect this week.
One of the conditions for this was that boards would not intervene to lower forecast growth rates in the dispensing volumes during the term of the agreement, which expires in August next year.
Health boards could continue to take part in local initiatives which improved prescribing quality and patient outcomes, including medicines management and services in residential care facilities.
The boards' letter to GPs did not mention quality, Ms Young said.
"If the boards are saying it's not about volumes, they need to make it clear.
" There was nothing in the letter about making sure the right patient got the right medicine - "It is all about cost."
The guild viewed the matter seriously and if the boards did not "toe the line", it could prove a problem for the whole agreement across New Zealand.
Mr Rousseau said the letter to GPs was "precisely about prescribing quality and outcomes" and he failed to see what Ms Young was concerned about. He declined further comment.
District Health Boards New Zealand, which negotiated the agreement on behalf of boards, referred the Otago Daily Times back to the two boards for comment.
