The decision came after the commission, the European Union's executive arm, gave the six -- which also include Britain, Italy, Hungary and Romania -- a last chance in January to take steps to improve air quality or be hauled before the EU's top court.
However, EU Environment Commissioner Karmenu Vella told a press conference in Brussels that the countries, dubbed the "toxic bloc" by activists, had failed to act quickly enough.
"The commission had to conclude that... that the additional measures proposed are not sufficient to comply with air quality standards as soon as possible," Vella said.
"Consequently, the commission has decided to refer these (six) member states to the Court of Justice of the EU," the executive arm said.
The Luxembourg-based court can impose heavy fines.
Vella, who has called the pollution problem urgent and "life threatening," said Brussels feared it may end up waiting several more years before the countries put the right measures in place.
"We cannot wait any longer," he added.
The commission has been urging the wayward countries to establish incentives for the transport, energy and agricultural sector as well as improve urban planning and building design to improve on pollution.
Vella had also given Spain, the Czech Republic and Slovakia a last chance in January to start complying with EU standards, which he said they were now doing.
'Continental scale'
But he warned the commission was keeping the three under review.
In January, the nine countries were found to regularly exceed emissions limits set to protect Europeans against particulate matter and nitrogen dioxide (NO2), both pollutants.
Germany, Britain and France were targeted for failing to meet limits on NO2 while Italy, Hungary and Romania exceeded limits on particulate matter.
The EU estimates that air pollution costs the bloc 20 billion euros ($24.7 billion) a year in health costs, but says this could be reduced if member states comply with agreed emissions limits.
Throughout the EU, fine particulates -- small particles of pollution -- were responsible for three out of four premature pollution deaths (399,000 out of 487,600) in 2014, according to EU figures.
The European Environmental Bureau, an umbrella grouping of activists who dubbed the nine countries summoned in January a "toxic bloc," welcomed the commission's action.
"Today’s announcement should surprise no one, the countries being sent to court have had too many final warnings," the EEB's Margherita Tolotto said.
"European air quality laws are being broken on a continental scale," Tolotto said.
But Tolotto said the process behind legal action should be "far more transparent" to allow citizens to know why some countries were taken to court and others not.
The problem is also broader than with the nine countries, if not quite as dramatic.
Twenty-three of the 28 EU member countries exceed air quality norms, the European Commission said.
The problem affects more than 130 cities in Europe. Bulgaria and Poland, which have also failed to take action, have already been taken before the top court.
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