Mr Thomson, who is chairman of the Otago District Health Board, would prefer funding distributed through primary health organisations (PHOs).
This was ruled out in a report exploring new ways of funding pharmaceuticals in the community, on the grounds it would breach the Commerce Act.
Mr Thomson told Thursday's monthly board meeting that sending out questionnaires seeking submissions about the Otago and Southland Community Pharmaceuticals Initiative should be delayed until Commerce Commission advice had been sought directly.
The two district health boards have been looking at pharmacy funding in a bid to reduce the burgeoning community drugs bill.
In Otago, it makes up 11% of the board's health budget.
Management's preferred option was one in which the board would bulk-fund participating pharmacies for dispensing fees.
Pharmacies and PHOs and general practices would be encouraged, through incentive payments, to work collaboratively to make the most of community pharmaceutical expenditure, cutting down on any wasteful practices and ineffective treatments.
The changes would not affect the way people got prescriptions or paid fees to their doctors or pharmacies.
The amount of money saved, however, would be affected by the number of pharmacies participating, since involvement would be optional.
Public comment on the proposal to date has not been favourable, with the pharmacy guild suggesting it could pit GPs and pharmacies against each other and doctors taking issue with any implications they are overprescribing or prescribing unnecessarily.
Under the PHO model favoured by Mr Thomson, participating PHOs would hold the money for pharmacy professional services and contract pharmacies to provide dispensing services.
PHOs would then distribute savings made to participating general practices and the pharmacies.
It was considered this would breach the Commerce Act because of price-fixing implications (from which boards have an exemption), possible anti-competitive behaviour if pharmacists were on PHO boards and involved in discussions regarding their contracts, or when community pharmacists collaborated over their funding and contracts.
There would also be difficulties if the board attempted to insist all pharmacies be funded through the PHO.
Mr Thomson said there was price fixing now and the Commerce Commission was aware there were issues in health which were different from those in the private sector.
If the commission was approached, it might tell the board to "go away and make a $150,000 application and get lawyered up the eyeballs" and the board would need to think about that, but it was worth seeking its opinion.
Many things were being done well in primary health care, but one thing it had failed to do was bring together parts of community health such as GPs, pharmacies and practice nurses.
The PHO funding model could do that.
" A lot of this would be much less threatening if driven from within PHOs."
The board agreed to delay the decision on seeking submissions until management had consulted the Commerce Commission about the likely difficulties of the PHO option and whether they could be resolved.
Board members Peter Baron, Dr Branko Sijnja and Dr Malcolm Macpherson declared an interest and did not participate in the discussion.
The existing funding system - Pharmacies receive $5.16, plus GST, for every subsidised item they dispense.
Bulk-funded models - Pharmacies would receive fortnightly fees based on their historical expenditure.
