Ten of the EU's 15 states overshot national targets, increasing total emissions by 1 percent in the last year for which data is available.
The figures threaten to blow a hole in the EU's ambitious climate change strategy, which has been sharply criticized by the United States and sections of European industry.
Under the 1997 Kyoto Protocol, which has been ratified by the EU, Japan and Canada but rejected by the United States and Australia, the Brussels-based club is committed to cutting greenhouse gases by 8 percent on their 1990 levels between 2008 and 2012.
EU emissions of the six main gases believed to be responsible for rising temperatures levels are still 2.3 percent below 1990 levels, but this is largely due to the dash to gas in Britain and industrial restructuring in eastern Germany during the 1990s.
The EEA says the latest increase is due to a cold winter in many EU countries, higher emissions from the transport sector and greater use of fossil fuels in electricity production.
Big increases were recorded in Austria -- up almost 5 percent -- and Finland, which saw emissions rise by 7.3 percent over 2000 figures.
However, it is Ireland, Spain and Portugal that are furthest away from meeting their share of the EU target.
Ireland's emissions in 2001 were 31 percent above 1990 figures, well over double the 13 percent increase it negotiated under the EU's 'burden-sharing' agreement.
Spain saw a modest drop in emissions between 2000 and 2001, but its output of greenhouse gases has still risen by almost a third since 1990. Emissions in Portugal have also risen spectacularly since the Kyoto treaty's base year.
The most dramatic cuts in gas emissions have been made in Britain, down 12 percent since 1990, Germany, down 18 percent and Luxembourg down a whopping 44 percent. France has managed to stabilize emissions from fossil fuels largely due to its reliance on nuclear power.
These largely positive figures are in sharp contrast to the United States, where emissions have jumped by over 20 percent since 1990.
Matthias Duwe, a policy adviser from the Brussels office of Climate Network Europe, said the EEA figures showed "the EU still has a long way to go to meet its Kyoto targets."
But Environment Commissioner Margot Wallstrom said Europe's greenhouse gas emissions could be slashed by over 15 percent if member states signed up to a raft of policy measures proposed by the EU executive.
"Our findings demonstrate that the Kyoto targets can be met without imposing unacceptable costs on society. Meeting them is a question of political will and full and effective implementation of the measures agreed," said Wallstrom.