Just one area - Tayside - consistently recorded at least 98% of people being seen within four hours, according to official figures for the first three months of this year.
Five of the country's 14 boards hit the benchmark in March.
The update comes weeks after an in-depth Audit Scotland report prompted concerns about the length of time patients are being forced to wait in A&E departments.
The latest figures show 93.3% of patients were seen within the target in March, down from 93.5% in December.
But over a full year, the average increased from 91.9%.
A second lower 95% target - set up in an attempt to drive forward improvements - was also missed by four boards in March.
Health Secretary Alex Neil said there are added pressures on the NHS during winter.
"Of course, we want to see more improvements, which is why the Scottish Government will continue to work with those health boards that need to deliver further improvement," he said.
"There is no question that our NHS is making sustainable progress towards delivery of the September milestone target of 95% of patients waiting no longer than four hours.
"In March this year, despite demand in A&E increasing by 6% - or 8,000 - compared to last March, the proportion of patients treated within four hours increased from 91.9% to 93.3%."
Audit Scotland, in its report earlier this month, revealed that about 104,000 people waited beyond the standard four-hour target in 2012-13, compared with about 36,000 in 2008-09.
In the 12 months to March this year, the total was 99,314, according to the new NHS figures.
Mr Neil said efforts to tackle waiting times over winter are paying off.
There were 2,713 fewer patients waiting more than eight hours between October and March than over the previous winter.
Scottish Labour MSP Neil Findlay said: "These figures again show that the SNP's waiting-times target is nothing but a fantasy.
"Despite our NHS staff working incredibly hard under huge pressures, the target has never been met across Scotland.
"Even when the SNP reduced the target, it still isn't being met in the majority of health board areas.
"Audit Scotland told the Scottish Government that our hospitals simply can't cope with the demands being placed upon them. These figures show that nothing has changed and that performance remains poor.
"Despite all the excellent work from our dedicated health professionals, our A&E departments aren't coping, even though the number of patients isn't increasing.
"The SNP's answer to systemic failure is to throw some cash at the problem. That's exactly what they did with A&E waiting times. It hasn't worked.
"This is more proof that we need a complete review of our NHS to make sure that it is fit for purpose for the 21st century. Patients and staff deserve nothing less."
Scottish Conservative health spokesman Jackson Carlaw said the Government is "miles away" from its target.
"This is a Scottish Government that is completely obsessed with the independence referendum, and its fascination with that is coming at the cost of performance in our hospitals," he said.
"The SNP needs to remember as well as trying to break up a country, it is meant to be running one too.
"Instead of constantly comparing our NHS to other places in the UK, it's time Alex Salmond focused on the performance here."