The crowd was protesting against comments that were misattributed to Alliot-Marie by the Arab service of Israeli radio after she met the parents of captive Israeli soldier Gilad Shalit.
Alliot-Marie was quoted as saying the European Union “must condemn the war crime that Hamas is committing by keeping Gilad Shalit in captivity”.
In fact, she had made no such statement, although Shalit’s father Noam had asked her to press the EU to condemn his son's captivity as a war crime.
Alliot-Marie said that the 1967 borders of Israel should be used by the EU as the basis of Isreali-Palestinian negotiations, in an invterview published in the Palestinian paper Al-Qods on Friday.
The minister has been in the Middle East since Thursday. She is visiting Israel, Egypt and Jordan.