The European Jewish Congress has demanded an apology and full retraction from Karel De Gucht following his comments.
Mr De Gucht, a former Belgian foreign minister, made the remarks in an interview in which he was asked about the resumption of direct peace talks between Israel and the Palestinians.
He said: "You cannot underestimate the weight of the Jewish lobby on Capitol Hill, the US Congress. It is the most well-organised pressure group over there."
He continued: "You also cannot underestimate the opinion, outside the lobby, of the average Jew who does not live in Israel.
"There is a conviction, and I can hardly describe it in another way, among most Jews that they are right. And conviction is something which is hard to combat with rational arguments.
"It is not easy to have, even with a moderate Jew, a rational discussion on the Middle East situation. It is a very emotional issue."
Moshe Kantor, the president of the European Jewish Congress, said: "Once again we hear outrageous anti-Semitism from a senior European official.
"The libel of Jewish power is apparently acceptable at the highest levels of the European Union. This should worry everyone who seeks a more tolerant Europe."
The European Commission distanced itself from the remarks, saying they were "personal views" that did not reflect the position of the EU regarding the Middle East peace process.
The row follows comments made by Thilo Sarrazin, a board member of Germany's Bundesbank, that "all Jews share a certain gene." Germany's president Christian Wulf is expected to dismiss Mr Sarrazin from the central bank because of his remarks.