More than nine in 10 family doctors questioned in a poll said they had been forced to write prescriptions for medicines that were not their preferred option.
One Scottish GP said doctors faced an "almost daily scramble around to find alternatives to common and heavily prescribed medications, and no real alternatives in some cases".
The survey of 635 family doctors by GP magazine found 93.5 per cent had been forced to prescribe a second-choice drug in the past year because of shortages.
When asked whether any patients taking second-choice drugs due to shortages have been negatively affected, including harm or a longer recovery, 7.4 per cent said many times and 28.5 per cent said yes, but rarely.
Four in five of those questioned said that drug shortages - for conditions ranging from conjunctivitis and acne to depression - had increased their workload in the last year.