In December there were 323 cases where patients in A&E had to wait this long, the highest number since July 2007, official statistics show.
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.
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 of discharged within four hours during December.
Health Secretary Alex Neil said it had been a "busy winter" for the health service, with the "additional complexity" of dealing with norovirus.
"We want to have as many people as possible treated within four hours of their admission to accident and emergency and we have to recognise that while the vast majority of people are, improvements can still be made," he said.
"There is no doubt that it was a busy winter with more emergency admissions than the same time last year and with the additional complexity of an early norovirus season.
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 announced that emergency and urgent healthcare services are to be given a £50 million overhaul to try to improve treatment times and patient care.
The money, available over three years, aims to change the way people are admitted to hospital, help them leave as soon as they are ready and improve links with other areas of healthcare so support is in place in the community.
Today Mr Neil said: "I have already made clear that we are taking significant action to improve unscheduled care in Scotland to make sure people are seen and treated in our hospitals and as quickly as possible.
"Changing the whole system takes time, which is why, as part of that investment package of £50 million, we will be doubling our winter planning fund to £6 million this year."
Opposition politicians hit out at the Scottish Government, with Tory health spokesman Jackson Carlaw criticising the "sloppy performance" on A&E waiting times.
Mr Carlaw, also the Conservative deputy leader, said the problem of patients waiting too long in A&E departments is "getting progressively worse".
He said: "Now we know the true extent of the crisis.
"The Scottish Government must explain why it was a whisker away from hitting these targets in past years, only to be now spectacularly missing them.
"This is the latest in Nicola Sturgeon's disintegrating legacy as health secretary, leaving her successor with an unenviable task of clearing up the mess she left behind.
"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.
"People would be forgiven for thinking the Scottish Government has lost the plot on A&E waiting times. But this sloppy performance is having a hugely detrimental impact on the well being of emergency patients across the country."
Liberal Democrat health spokesman Jim Hume blasted the "staggering drop in A&E units meeting waiting times standards".
Mr Hume said: "A day after the Health Secretary published his £50 million emergency care action plan to much media fanfare, these shocking figures show that compliance with the four-hour A&E waiting time standard is at the lowest since the SNP came into power.
"With such a big drop in compliance from November to December, this also raises questions about the success of the Scottish Government's winter contingency planning.
"In light of these figures, the Health Secretary will find it difficult to rubbish the stories of patients being left to languish on hospital trolleys."
Mr Hume said Liberal Democrats would press Mr Neil to set a clear timetable for allocating the emergency care action plan funds announced yesterday.
Labour health spokeswoman Jackie Baillie demanded "real action rather than press releases and excuses" from ministers.
"Patients are now paying the price for the SNP's failure to address the underlying problems in our NHS," she said.
"While it's clear that Alex Neil's winter planning measures were woefully inadequate, resulting in December having the worst set of waiting times figures in more than five years, this is also part of an ongoing downward trend.
"This SNP Government is not meeting it's own A&E waiting times and these are now the worst figures since the SNP were elected.
"How can Alex Neil expect to meet the growing demand at a time when his Government has cut almost 1,500 beds and thousands of nurses?
"We cannot continue to ask NHS staff to do more with less and not expect consequences for patients. We need real action rather than press releases and excuses."
Meanwhile, new figures have revealed that assaults accounted for 4,400 emergency admissions to hospital last year.
Blade attacks made up a fifth (21%) of the admissions in 2011-12, according to NHS statistics, which is down 30% since 2006-07.
Assaults accounted for 72 deaths in 2011, of which 51 were the result of attacks by a sharp object. This marks a 15% drop from five years previously.
"Unintentional injuries" were responsible for 54,427 emergency admissions last year, accounting for one in seven child admissions and 1 in 10 for adults.
Producers of the statistics, Information Services Division Scotland, use the term rather than "accidental" as they say this implies something unavoidable, while most injuries are preventable.
Of the admissions due to unintentional injuries, around 32,000 or 60% were the result of falls.
Nearly half (49%) of them were aged under 15, with most suffering from fractures and head injuries.
Children living in the most deprived area were more likely to be admitted to hospital for an unintentional injury.