The Commission, the European Union's executive arm, gave the six, also including Italy, Hungary and Romania, a last chance in January to take the required steps to improve air quality after years of warnings.
However, EU Environment Commissioner Karmenu Vella told a press conference in Brussels the six, which include Europe's top four economies, had not acted 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, and therefore are being referred to court," Vella said.
"We cannot wait any longer," Vella said, warning that Brussels may end up waiting several more years before the countries put measures in place.
Vella had also given Spain, the Czech Republic and Slovakia a last chance in January to start complying with EU standards and decided to give them a reprieve.
"The measures that are planned or being put in place appear to be able to tackle (exceeded limits) if they are fully and immediately implemented," Vella said.
But he warned the commission was keeping the three under review.
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 commission has been urging the wayward member countries to establish incentives for the transport, energy and agricultural sector as well as improve urban planning and building design.
The European Environmental Bureau, an umbrella grouping of environmental activists, has described the nine countries summoned in January as a "toxic bloc".
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