Some departments have been particularly badly hit. More than 12% of emergency medicine posts are unfilled, as are almost 18% of acute medicine positions.
The gaps were revealed along with a raft of other statistics which paint a mixed picture of NHS performance in Scotland.
According to the new data, published by the statistics arm of NHS Scotland yesterday, there are 222 vacancies for medical consultants, representing 4.7% of posts.
This is up from a low of 2.8% in June 2011.
Targets for A&E waiting times and for ensuring patients well enough to go home are discharged within six weeks have both been missed.
Scottish Labour's health spokesman Neil Findlay accused the Scottish Government of "managing crisis after crisis rather than formulating any long term vision" for health boards.
He said: "I have called for the Scottish Parliament's health committee to hold an inquiry into the NHS in Scotland and ensuring there is sufficient staff in place should be central to this investigation. Staff and patients deserve better."
Signs that Scottish hospitals are under growing pressure have been highlighted in a series of articles published by The Herald and the newspaper is calling for a review to ensure the right staff and beds are in place in both hospitals and communities to look after the growing elderly population.
A spokeswoman for the British Medical Association in Scotland said: "There are some specialities where it is becoming particularly difficult to fill middle grade roles and we are already starting to see the impact of that on the provision of services - for example services in West Lothian having to temporarily close last year."
The new A&E waiting times figures showed 94.6% of patients in June being dealt with within four hours. However, 313 patients waited more than eight hours in A&E and 25 more than 12 hours. The number of patients seeking treatment via A&Es appears to have risen since the winter, but they are also being discharged or found ward beds more quickly.
Bed blocking, where patients are well enough to go home from hospital but can't leave because the necessary community care is not in place, is thought to be behind some capacity problems. The latest check shows 59 patients spending more than six weeks in hospital beds after they were well enough to be discharged - more than the same time last year.
Health Secretary Alex Neil yesterday announced the release of £6.8 million to support A&E departments, saying: "As we continue to deal with the requirements of an ageing population, we are seeing an increasing requirement for more effective unscheduled care.
"That is why we continue our actions to improve unscheduled care in Scotland and this latest funding will help to ensure people are seen quickly and treated effectively."