Audit Scotland found that the number of patients waiting longer than four hours in A&E almost tripled from 36,000 in 2008/09 to around 104,000 in 2012/13.
It also found average waiting times have increased to over two hours, with tens of thousands of patients only being seen as they were about to breach the four-hour target set by the Scottish Government.
Opposition parties called for urgent action to improve deteriorating performance in emergency units, which has been linked to pressure on beds and staffing levels across hospitals as well as rising demand and the ageing population.
A target set by the Scottish Government stated that by the end of 2007, 98 per cent of patients in A&E or minor injury units (MIUs) should wait no longer than four hours before being discharged or admitted.
But following a challenging winter season which saw long waits across A&E units in Scotland, in April last year Scottish ministers introduced a new “interim target” of 95 per cent attainment by September this year.
In 2010, an Audit Scotland report said NHS boards had improved the way they tackled longer A&E waits but faced challenges in maintaining the four-hour standard.
But their latest report said: “Since then, A&E departments’ performance against the standard deteriorated and during winter 2012/13 performance fell to the lowest it has been since the standard came into effect.”
In December 2009, 97.2 per cent of patients were seen within four hours. But by December last year, despite an improving picture in the previous 12 months, this stood at 93.5 per cent. The lowest point came in January 2013, when only 89.7 per cent of patients were seen within four hours.
While some hospitals have performed well, even against the higher 98 per cent target, others have continued to “perform poorly”, the report said, including Edinburgh Royal Infirmary (ERI), Glasgow Royal Infirmary and Wishaw General Hospital.
The figures also showed rising attendance in A&E and MIUs, up from 1.57 in 2008/09 to 1.62 in 2012/13. Audit Scotland said this rise was due to increasing attendances at MIUs, while A&E visits were down 1.4 per cent to 1.35 million.
But the report said that the focus on reducing delays over four hours meant less attention was given to the increasing average time patients were spending in A&E.
“There is an underlying trend of patients generally waiting longer in A&E,” Audit Scotland said.
“The median wait across A&E departments has increased from 99 minutes in 2008/09 to 126 minutes in 2012/13.”
They also found evidence of patients being treated just before they breach the four-hour target.
In 2012/13, 70,000 patients (5.3 per cent of all attendances) were dealt with in last ten minutes of four hour period, up from 45,000 (3.3 per cent) in 2008/09.
Audit Scotland went on to explore the reasons for deteriorating performance in A&E.
It found that in 2012/13, 38 per cent of delays in A&E were reported as being due to waiting for a bed elsewhere in the hospital, while 21 per cent were linked to waiting for a first full clinical assessment.
An increase in patients admitted to hospital from A&E - up 8 per cent from 334,879 in 2008/09 to 361,121 in 2012/13 - has meant growing pressures on beds.
Three reasons accounted for nearly 70 per cent of delays in A&E – waiting for a bed, waiting for a first full clinical assessment and waiting for a specialist, the report said,
The report also highlighted high occupancy levels in many hospitals. In 2012/13, six boards had average occupancy rates over 85 per cent. Research shows higher risks in units with over 85 per cent occupancy. Boards with higher occupancy rates performed worse against the four-hour target.
Auditor General for Scotland Caroline Gardner said: “Delays in A&E can be a sign of pressure across health and social care.
“While there has been improvement in performance, such as the progress made in tackling the longest waits in A&E, performance against the target still remains lower than it was when we last reported.
“It is important that the Scottish Government and NHS boards build on their whole system work and continue to reduce delays for A&E patients.”
Scottish Labour’s Neil Findlay MSP, said: “This report shows that our hospitals are simply unable to cope with the growing pressures they face, when combined with the cuts to staffing and beds which have been imposed by the SNP.”
“The SNP’s A&E targets haven’t been met across Scotland since 2007. Even when they reduced the target, we still see many health boards struggling to meet it.”
Conservative health spokesman Jackson Carlaw added: “This report makes it perfectly clear that a lack of staff is one of the reasons departments struggle, and it’s notable that the Scottish Government began slashing numbers about the same time casualty performance began to decrease.”
Hugh Henry, convener of Holyrood’s Public Audit Committee, said the report was “extremely worrying”.
“We all know the complexity of A&E services but by now we should have been seeing signs of progress,” he said.
Dr Nikki Thompson, chair of the British Medical Association’s Scottish Consultants Committee, said: “This report illustrates the extreme pressures A&E departments are working under while dealing with rising demand and an ageing population.
“Workforce shortages and high vacancy rates are a significant contributing factor. As a result, medical staff are working under considerable strain to try to maintain high quality care in an overstretched system; clearly this is not sustainable.”
The Scottish Government said significant improvements had been made in the first year since it launched its £50 million action plan for emergency care.
Health Secretary Alex Neil said: “We have already invested heavily – both in service improvements and more staff.
“That includes the 18 new consultants now appointed across NHS Scotland.
“This builds on the increase under this Government, which has seen the number of A&E consultants has more than double, from 75.8 to 162.3 since 2006.”