More than 300 patients were kept waiting in A&Es for more than 12 hours this December and one in 10 were there for more than the target time of four hours.
The new figures were among a raft of statistics on waiting times likely to cause additional embarrassment to the Scottish Government after it faced allegations about NHS performance results being manipulated last week.
They also showed 85 patients waiting for planned hospital treatment for longer than 12 weeks – even though the SNP made this waiting times target legally binding in the autumn.
The number of people who spent more than 12 hours in A&E in December was the highest on record at 323.
Two patients in NHS Lothian and five patients in NHS Ayrshire and Arran waited more than 12 weeks for procedures in the last months of 2012.
A further 78 appeared to have waited more than 12 weeks at the end of the year, although the Scottish Government said some of these patients had been seen and the figure would be revised.
Jackie Baillie, Scottish Labour's health spokesperson, said: "Patients are now paying the price for the SNP's failure to address the underlying problems in our NHS.
"While it's clear that [Health Secretary] 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."
Public spending watchdog Audit Scotland last week published the results of an investigation which raised concern that health boards had taken advantage of social unavailability codes, which allow patients waiting for planned operations to be suspended from waiting lists.
The practice of marking patients as socially unavailable to make their figures look better had already been exposed at NHS Lothian and it has been struggling to deal with a backlog of patients since the reality of demand was revealed.
NHS Forth Valley is only treating 83.3% of patients within the target. Audit Scotland revealed that Forth Valley staff had been marking some patients suspended from the list as "aware of [target] breach – willing to wait". Up to one-quarter of those listed as unavailable had been given this code until the practice was stopped last May.
Mr Neil, who has adamantly denied widespread manipulation of waiting list figures, said it was good to see 58,000 people across Scotland benefiting from the new legal waiting time guarantee.
However, he added that he wanted 100% of patients to receive treatment in the target time frame.
It is understood health boards have to write to patients with an explanation if they do not deliver on this goal and give them the next suitable appointment slot.
Mr Neil also admitted improvements "can still be made" to A&E waiting times.
He added: "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 [winter vomiting bug] season.
Scottish Liberal Democrat health spokesperson Jim Hume urged Mr Neil to set out a time-table for his emergency care action plan, describing the latest A&E results as staggering.
He said: "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."
Scottish Conservative health spokesman and deputy leader Jackson Carlaw MSP said: "The Scottish Government must explain why it was a whisker away from hitting these [A&E] targets in past years, only to be now spectacularly missing them."