Dr Brian Keighley, the chairman of the British Medical Association, said politicians and health service managers must look at how services can be made more efficient, and where cuts could be made without affecting patient care.
Derek Feeley, the chief executive of NHS Scotland, hailed the service's best-ever performance in key areas over the past year.
Dr Keighley said: "The fact the NHS in Scotland has delivered such a high standard of performance is testimony to its hard-working staff who find themselves under increasing pressure to achieve targets whilst staffing numbers and budgets fall.
"It is through their hard work and commitment that the NHS can deliver care of the highest standard.
"Our NHS is facing tough times and, as financial pressures mount, tough choices will need to be made about what the NHS can and cannot afford to deliver."
But Dr Keighley said doctors were best placed to provide strong clinical leadership and identify waste and efficiencies.
Achievements highlighted in Mr Feeley's annual report include meeting the target of having 90% of patients wait no longer than 18 weeks from referral to treatment.
Cancer waiting times, including reducing the time between the decision to treat a patient and that treatment starting to 31 days, have also been met.
There has been a 24% fall in C.diff cases, as well as a 10% reduction in MRSA/MSSA cases in 2011-12.