Just two of Scotland's boards achieved the four-hour admittance, transfer or discharge target for 98% of patients.
Both NHS Tayside and NHS Shetland met the target from June to September.
Five areas, including NHS Fife, NHS Orkney and NHS Western Isles, achieved the standard in September.
But across Scotland seven of the 14 health boards – Greater Glasgow and Clyde, Lanarkshire, Ayrshire and Arran, Dumfries and Galloway, Forth Valley, Grampian and Lothian – did not achieve it.
NHS Greater Glasgow and Clyde said it was taking steps to help staff meet the target.
Across Scotland in September 95% of patients in A&E were either admitted, transferred or discharged within the four hour target time.
The same figures also revealed that the total number of A&E attendances increased from 1.5 million in 2001-02 to 1.6 million in 2011-12.
Meanwhile, figures show "bed blocking" within the NHS is increasing.
The total number of bed days occupied by delayed discharge patients was 121,948 between July and September.
The figure is a 2% increase on the previous quarter.
NHS Lothian has the highest rate, followed by NHS Lanarkshire.
A Scottish Government spokeswoman said: "We have made great progress over the last six years in reducing delayed discharges, yet too many people, mainly older people, are still waiting too long to be discharged from hospital.
"That is why we have set even tougher targets: to have no-one delayed for more than four weeks by 2013 and more than two weeks by 2015."
Labour said there is a "lack of basic planning" between the NHS and councils to sort out care packages for patients waiting to be discharged.
Today's official figures also reveal a slight increase in the number of NHS staff in Scotland over the last year.
Including GPs and dentists, the total was 162,234 in September, 883 more than the same month last year.
Nurses and midwives decreased over the year by 68 to 65,448, prompting concerns from Labour about funding.
Labour health spokeswoman Jackie Baillie said: "There are fewer nurses in the NHS in September this year than a year ago and the SNP now have fewer nursing staff than when they came to power in 2007.
"The NHS can't go on like this. It is getting by on a month-by-month, year-by-year basis, with no strategic planning."