The justice system currently relies on NHS doctors who are paid to work with the police, carrying out work such as examining victims of physical and sexual assaults and collecting samples for DNA testing.
But BMA Scotland said time wasted due to re-scheduled court appearances where they are called to give evidence left many doctors concerned about the impact on patient care.
The trade union said there was anecdotal evidence that clinicians were already withdrawing from the work amid frustrations which “must be addressed”.
It followed a submission to an ongoing inquiry into the work of the Crown Office by forensic medical examiner Dr Gary Cooney.
Writing to the Scottish Parliament’s justice committee, Dr Cooney said that many of his colleagues had already turned their back on the police work.
He said: “As I work full-time within the NHS, during normal working hours an attendance in court requires that I arrange for another doctor to cover my clinical commitments.
“I know of several examples of clinicians deciding to discontinue their work as forensic medical examiners as a result of the frustrations they have experienced with timings and scheduling of court appearances.”
A BMA Scotland spokeswoman said: “Doctors provide an invaluable service when called to give professional evidence to assist our courts. But it is imperative that steps are taken to ensure disruption to their clinical roles are kept to a minimum.
“Time wasted establishing whether there is a requirement to attend court is stressful for doctors who are already dealing with unprecedented pressures and this could have a knock-on effect on that individual’s availability to provide patient care.
“There is anecdotal evidence to suggest clinicians are deciding to discontinue their work as a result of their frustrations, which is concerning and must be addressed.”
A Crown Office spokesman said: “As prosecutors we always endeavour to minimise, where we can, the inconvenience to any witness during criminal proceedings.”