WWF Scotland said analysis of Scottish Air Quality data from 2011 showed levels of nitrogen dioxide (NO2) in parts of Aberdeen, Dundee, Edinburgh, Glasgow and Perth were in breach of European Union targets of 40 micrograms per cubic metre of air designed to protect health.
European leaders are aiming to make 2013 the “Year of Air” to highlight the problems of pollution and air quality.
WWF Scotland is now calling on the Scottish Government to take urgent action to address the issue.
Dr Dan Barlow, its head of policy, said: “It is totally unacceptable that Scotland has breached European air pollution targets for the second year in a row.
“As a result of a complacent approach, thousands of people are exposed to dangerous levels of air pollution in Scotland’s major cities.
“Scotland has had plenty of time to take preventative action, so it is shocking that we have failed to put in place the measures needed to meet air quality targets and protect human health.
“This situation is a direct result of the failure of successive governments to produce a sensible strategy that adequately addresses air pollution and climate emissions from road traffic.”
The news comes at a time when it is being suggested Scotland may not meet air quality targets until 2020.
Dr Barlow said: “Government investment and infrastructure plans are set to prioritise road building over public transport improvements and cut funding for walking and cycling.
“Improving air quality and tackling climate emissions requires a shift in government transport spending plans to place much more emphasis on sustainable solutions.”
Discussions are taking place at EU level about launching the “Year of Air” programme to help cities across Europe achieve the “holy grail” of ensuring air pollution does not pose any significant risk to human health and the environment.
Janez Potonik, European commissioner for the environment, says the proposal has already been debated with EU chiefs and European Commission president Jose Manuel Barroso.
The average life expectancy in the most polluted cities in Europe is reduced by more than two years, EU chiefs have estimated.
In economic terms, it has been estimated that the cost to society across Europe of health damage from air pollution in 2000 was somewhere between €277 billion (£230bn) and €790bn.
Initiatives to highlight the “Year of Air” are likely to include the early introduction of clean vehicles in urban areas with air quality problems as part of demonstration projects and the greater promotion of retro-fitting old vehicles with new “air-friendly” technology.
The Scottish Government said it had set out a vision to make the country’s roads as efficient as possible.
Work was also under way to develop low-carbon vehicle technology, promote “active travel choices” and encourage a shift towards public transport.
A spokesman said: “We are also making considerable investment in inter-urban connectivity across road and rail, illustrated through the recently completed M74 extension and Airdrie-Bathgate rail link.
“These types of investment are making a real difference to travel choices and journey times.”