The industry body said that significant drop offs in a few, previously healthy, markets are to blame for the fall.
Spain, formerly a market leader with the second highest wind capacity, saw its installations fall by 84%, following changes in tax and subsidy regulations.
The Italian and French markets were also hit, with installations falling 65% and 24% respectively.
This has resulted in 45% of all installations being made in just two countries – Germany and the UK.
EWEA said this represented a worrying trend towards greater concentration of installations and away from a previous dynamic where they were being "increasingly spread across healthy European markets".
There are now 116.8GW installed in the European Union, providing 8% of the region's energy, EWEA said.
"Destabilised legislative frameworks for wind energy have undermined investments, and put green growth, jobs and energy security at risk," said Justin Wilkes, EWEA deputy CEO.
Despite the downbeat message, EWEA also pointed out the wind power installations in 2013 accounted for 31% of total power capacity installations, more than any other technology.
Offshore wind was also a source of some solace, and saw record growth in 2013, with 1.6 GW added. EWEA said it expects the offshore market to remain stable, but not to grow in 2014 and 2015.
Earlier in January, the EU excluded a binding renewable energy target from new emissions-reduction proposals.
EWEA had been pushing for the inclusion of country-specific renewables target for 2030, similar to the 2020 goals.
But while EU president José Manuel Barroso announced a proposed target for 27% renewables by 2030 for the whole of the EU, countries will only set targets "if they wish".
There is now 116.7GW of installed wind energy capacity in the EU, 110GW of which is onshore and 6.6GW offshore.
