Meeting in the shadow of the Acropolis, birthplace of democracy, the ministers resolved last week to make "intercultural" education an "important component" of school life and teacher training.
The wars of nationalism since communism was swept away, tension between West and East since September 11, economic migration and persistent prejudice against some minorities such as Roma have combined to make the building of tolerance to different cultures a challenge in classrooms across Europe.
Maud de Boer-Buquicchio, deputy secretary general of the Council of Europe, said: "Ignorance and prejudice often result in diversity, especially religious diversity, being seen as a threat." She said education about other cultures could help stamp out racist violence and other forms of intolerance.
Experts praised examples of best practice in Scandinavia and Britain, where there was an emphasis on not only tolerance and understanding but on collaborative learning between children from different backgrounds and where pupils were given a say in running schools through elected councils.
The Greek minister for education and religious affairs, Petros Efthymiou, host and president of the conference, highlighted valuable work to remove inflammatory language from history textbooks in the Balkans and south-east Europe.
He was challenged on the case in Greece of a top-performing Albanian pupil who was prevented from taking up the legal right of the best students to carry the Greek flag into class by protesting parents. He said the boy's right must be upheld or it would push minorities into "ghettos", he said.
Pieter Batelaan, editor of the magazine Intercultural Education, said that while governments worry about political problems caused by ethnic tensions, teachers' concerns are more deep-rooted, focusing on issues that affect the personal development of each individual child.
"The ministers' declaration is an instrument that teachers can show politicians and say 'This is what you agreed'," he said.
The conference of European education ministers meets every three years.
Council of Europe education programmes have included ones to promote democracy in former communist countries and tackle intolerance of Roma children.