In December there were 323 cases where patients in A&E had to wait this long, the highest number since July 2007.
National standards in Scotland set out that at least 98% of people in A&E should be either admitted or transferred for treatment, or discharged from hospital, within four hours of arrival.
Across Scotland, just 90.3% of patients were dealt with within the target time in December, down from 95% in September and the lowest rate recorded since July 2007.
In the NHS Lanarkshire area just 84.4% of patients in A&E were admitted, transferred or discharged within four hours during December.
NHS Greater Glasgow and Clyde fared better, with an average of 90%. However this was down from 95% in October and November.
Target rates varied widely across hospitals, from 83% at the Western Infirmary to 100% at the Minor Injuries Unit at Stobhill. Health Secretary Alex Neil said it had been a "busy winter" for the health service, with the "additional complexity" of dealing with norovirus.
He said: "We want to have as many people as possible treated within four hours of their admission to A&E and we have to recognise that while the vast majority of people are, improvements can be made."
Only four of Scotland's 14 regional health boards met the A&E waiting time target in December: NHS Orkney, NHS Shetland, NHS Tayside and NHS Western Isles.
The figures were disclosed the day after Mr Neil unveiled a £50 million plan to speed up emergency treatment in Scotland's hospitals.
The plan will include more doctors specialising in A&E treatment and increased use of minor injury units.
Jackson Carlaw, Conservative health spokesman, criticised the "sloppy performance" on A&E waiting times. He said the problem of patients waiting too long in A&E departments was "getting progressively worse". Mr Carlow added: "Now we know the true extent of the crisis.
"It is a complete disgrace that in some parts of Scotland more than 15% of patients are being left to languish for more than four hours."
Liberal Democrat health spokesman Jim Hume blasted the "staggering drop in A&E units meeting waiting times standards".