The rise in vacancies among allied health professionals is part of what Labour branded an “NHS staffing crisis”.
The same data also revealed the number of consultants posts unfilled for six months or more has risen by almost a fifth in the last year.
Almost two thirds (61.9 per cent) of consultant vacancies have been empty for at least half a year.
According to the latest figures the health service in Scotland employed the whole time equivalent (WTE) of 139,095.2 workers at the end of June this year - a rise of 0.1 per cent over the last 12 months.
The NHS data showed that while there have been six consecutive years of increases in staffing, the rate of growth had now slowed.
By 30 June there were 5,261.4 WTE consultants in post, an increase of 2.4 per cent from the previous year.
The vacancy rate was down from 8.5 per cent in June 2017 to stand at 7.6 per cent, with 433.7 WTE posts unfilled.
But of these 268.7 WTE jobs had been vacant for at least six months - an increase of 17.9 per cent on the June 2017.
Doctors branded the rise in long term vacancies as “deeply troubling” and said it showed health boards were struggling to recruit doctors to these posts.
Simon Barker, chair of BMA Scotland’s consultants committee, said: “The NHS will not be able to muddle through with an inadequate numbers of consultants who feel unvalued. People in Scotland deserve better.”
The vacancy rate for nursing and midwifery jobs was 5.3 per cent in June 2018, with 3,311.2 WTE positions empty.
Staffing figures showed 59,455.9 WTE nurses and midwifes working in the NHS, up by 0.1 per cent on June 2017.
Meanwhile there were 11,604.1 WTE allied health professionals - which also includes podiatrists and speech and language therapists - working in the NHS in Scotland.
Vacancies for such positions reached a record high of 4.8 per cent, the figures showed, with 588.4 WTE posts unfilled, compared to 543.4 WTE in June 2017.
Labour health spokesman Anas Sarwar said: “The SNP government cannot blame the current situation on Brexit, it is a staffing crisis made in Scotland by the SNP.”
Tory health spokesman Miles Briggs said: “Scotland’s NHS is under extreme pressure, and this is largely because we’re short of more than 3000 nurses and midwives.”
Health Secretary Jeane Freeman highlighted the six consecutive years of growth in workforce numbers.