Synagogues have been attacked across France
Justice and interior ministers meeting in Luxembourg condemned "all forms of intolerance which take as their pretext the conflicts and acts of violence in the Middle East and are aimed at persons of the Muslim, Jewish or any other faith".
The statement comes after a spate of attacks on Jewish targets in France and Belgium in which several synagogues were firebombed.
They coincided with a surge in anti-Israeli feeling, particularly amongst the Muslim community, over the military campaign against Palestinians in the West Bank.
The meeting condemned the attacks and called for closer co-operation between EU police forces.
"At a time of acute international tension, especially in the Middle East, it is vital to preserve the spirit of harmony, entente and inter-cultural respect within our societies," a statement said.
It also urged the European Commission to propose steps to "raise public awareness of what is at stake".
Asylum move
Thursday's meeting was scheduled before French far-right presidential candidate Jean-Marie Le Pen visited Brussels on Wednesday.
Mr Le Pen, who faces incumbent Jacques Chirac in the presidential run-off on 5 May, was heckled by deputies in the European Parliament who held up signs saying "no".
The National Front leader has in the past described the genocide of Jews in the Holocaust as a detail of history.
But the Luxembourg talks were based on a declaration made earlier in April by France, Britain, Germany, Spain and Belgium.
The ministers also took the first steps towards setting up a co-ordinated EU asylum policy.
They agreed to establish the same reception standards across all 15 states in an attempt to stamp out "asylum shopping" - applying for refugee status in the individual European countries with the best perks for asylum seekers.
They aim to have the same minimum standards of housing, education and health for asylum seekers across Europe.
They also pledged to speed up the application procedure.
The common policy should be in place by 2004.