The move by NHS Forth Valley to allow a community pharmacy to open in the same village as Drymen Health Centre, east of Loch Lomond, means the surgery will lose the capacity to dispense medicines.
Dr Jennifer Foster, the only permanent doctor at the surgery, said the loss of income would mean she had no choice but to reduce opening times, leaving patients to travel up to seven miles in an area with poor transport links to access GP and nursing services when her surgery is shut.
It follows a similar dispute on the island of Cumbrae, where local GPs quit after a pharmacy opened nearby.
Meanwhile, GPs have also opposed a proposed new pharmacy in Aberfoyle.
Dr Foster described the decision to allow the application in the face of strong local opposition as "a travesty" and said patients had been left "shocked and appalled" by the ruling of the health board's Pharmacy Practices Committee.
However, Paul Pollock, a director of Drymen Potions Ltd, which is behind the application, said his pharmacy would benefit the local population overall, as people not signed up to Dr Foster's practice are unable to access any pharmacy services in the village.
Dr Foster, who has served the community for two decades, said closing her surgery for three half-days a week was likely to be the "best scenario" and that two dispensary employees, as well as five permanent staff, now faced uncertain futures.
"I'm extremely disappointed," she said. "The views of the public have not been listened to. The crux is now that the health centre is going to be closed for part of the week. The health board knew that.
"It seems it's okay for patients to have to go to another village for GP or nursing care but not for a pharmacy. For small rural practices in Scotland the way we are paid does not generate enough money to pay for staffing."
A petition against the application, signed by 326 people, has been submitted and it was accepted that travelling to practices in neighbouring villages would be particularly tough for those who rely on public services, young mums and the elderly.
But the committee concluded that granting the application was "necessary and desirable" after deciding current provision was inadequate.
The Scottish Government said a consultation over national regulations stating that GPs are only allowed to dispense drugs in communities where there is no pharmacy had recently concluded and the results would inform amendments to regulations.
Mr Pollock, who plans to open his community pharmacy within six months, said: "We want to allow the doctor to do their job, which is diagnosing and treating conditions, while we do the job of a pharmacy.
"We appreciate the doctors practice is saying it may have to tighten belts but we feel we will bring an overall benefit."