LMCs warned the change could undermine attempts to cut unnecessary antibiotic prescribing.
GPC Northern Ireland chairman Dr Brian Dunn said that since the scheme ended at the start of August, GPs have seen a rise in attendances by patients with minor ailments.
Since 2005, the bulk of these patients had been redirected for treatment by 500 community pharmacists.
In Craigavon, where take-up of the service was high, Southern LMC secretary Dr Arnie McDowell said: 'The suspension of this valuable scheme creates pressures for us.'
Practices had worked hard to make the scheme a success, he said, but hopefully the suspension was only a 'temporary blip'.
'The danger now is that people will go back to old habits, and in returning to GPs for minor problems, there will be greater pressure for GPs to prescribe antibiotics,' he added.
Since the scheme's launch, there have been around 250,000 consultations with pharmacists. The service was designed to save the NHS money by reducing visits to GPs.
Initially, pharmaceutical advice and treatment for coughs, colds and hayfever were provided under the scheme for patients exempt from prescription charges.
But the scheme collapsed after Northern Ireland's Department of Health, Social Services and Public Safety wrote to pharmacists in July asking them to enhance the service to include treatments for head lice, diarrhoea, dhobie itch, athlete's foot, vaginal thrush and threadworms.
The two sides were unable to reach an agreement on extending the arrangements, and pharmacists withdrew the service with effect from 1 August.
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