One board has witnessed a sevenfold rise in incidents, amid expectations that the true scale of the problem is actually much higher.
NHS Lothian, which was at the centre of a waiting-times scandal, recorded 1888 violent incidents against its employees last year.
This compares with only 274 in 2009, and means more than five of its nurses, doctors, secretaries and other administrative staff were assaulted each day last year.
This year a further 134 staff were attacked by January 18 – more than seven every day. The board faced controversy for removing patients from waiting lists if they refused treatment in England.
Dr Malcolm Bruce, a member of the BMA's Scottish consultants committee and a consultant psychiatrist, said: "The numbers of cases reported at NHS Lothian are disappointingly high, but it could be down to better reporting rather than an increase in violence against staff.
"Nevertheless, it is completely unacceptable that NHS staff are subject to physical or verbal abuse while they are going about their jobs.
"Unfortunately, we know from our own research that most cases of physical or verbal abuse go unreported, so it is likely that the number of cases is much higher, not just in Lothian but across Scotland."
Lanarkshire has also experienced a sharp rise in attacks on its staff. Between 2009/10 and 2011/12 the number of violent incidents recorded tripled, from 587 to 1740. Although reports have fallen back to an estimated 929 this year, that remains 58% higher than three years ago.
Greater Glasgow and Clyde, the largest board, suffered almost 5000 attacks on its employees so far this financial year, with the figure expected to increase to 5393 by the end of this month – up 16% on 2009/10.
Western Isles also saw cases of violence increase fivefold between 2009 and 2012, while NHS Fife is facing a 20% increase in incidents compared to three years ago.
Dr Richard Simpson, shadow minister for public health, said: "Increasingly, assaults and other more serious offences are being dealt with by fines – something which many Scots will rightly question. We also need to ask if longer waiting times, particularly in A&E, fewer beds, and fewer nurses, are a combination which increases the risk to staff."
Norman Provan, associate director of RCN Scotland, said: "There's under-reporting of violent incidents and by comparing what staff said in the last NHS survey two years ago, we'll have an up-to-date picture, directly from those on the frontline, about their experience of violence and abuse – and will hold to account those health boards with a poor record on violence against staff."
Alan Boyter, director of human resources and organisational development for NHS Lothian, said the authority had a robust reporting system and trained staff to manage threatening situations. He added: "We do not tolerate any form of violence or aggression towards our staff."
The Scottish Government said offenders faced up to a year in prison and/or a £10,000 fine.
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