The United States was just behind Israel in the global danger league, in joint second place with North Korea and Iran, according to the Eurobarometer poll requested by the European Commission.
The results released on Monday were part of a survey last month on Europeans' attitudes in the aftermath of the Iraq war.
The poll also found that more than two-thirds of EU citizens think the US-led war was wrong.
The response reflects the highly visible popular opposition to the war in nearly every European country before the US-led invasion.
The Israeli embassy in Brussels voiced outrage at the findings, which has said that 59% of Europeans see Israel as a threat to world peace.
"Europeans seem blind to Israeli victims and suffering. Instead, they have put the Jewish state below the level of the worst pariah state and terror organisations," it said.
"Israel's desperate struggle for peace and security for its people has been distorted beyond recognition in often one-sided and emotionally-charged media coverage"
"Israel's desperate struggle for peace and security for its people has been distorted beyond recognition in often one-sided and emotionally-charged media coverage," the embassy added.
The poll’s findings suggest Israel’s frequently deadly missile and armoured attacks on Palestinian urban areas, as well as air raids against its neighbours (such as last month’s air strike on Syria), are shaping the views of many Europeans.
But the EU's Italian presidency tried to play down the results, insisting they did not reflect the official EU position.
"The result of the survey, based on an ambiguous question, does not reflect the position of the European Union, which has been voiced on numerous occasions," Italian Foreign Minister Franco Frattini said.
"The EU is all the more annoyed since it is fully aware that the Israeli population is hit hard by terrorism," it said, criticising the "false signal" that the survey sent out.
Worries about Washington
According to the Eurobarometer poll, based on interviews with 500 people in each of the 15 EU states, about 59% of Europeans replied "yes" when asked whether or not Israel presents a threat to peace in the world.
US forces in action in Iraq: Self-
styled liberators seen as a threat
A total of 53% said Iran, North Korea and the United States pose a threat, followed by 52% for Iraq, 50% for Afghanistan and 48% for Pakistan.
Countries lower down the list included Syria, Libya, Saudi Arabia, China, India, Russia and Somalia. The EU itself was described as a threat by 8%of respondents.
The EU survey was presented in the form of a list of 15 countries, from which 7515 respondents were asked to say which ones they thought posed a threat to world peace.
Commission spokesman Gerassimos Thomas, repeatedly asked why the Palestinian territories were not included, replied: "It is not a country."
The European Commission said Israel's anger was "legitimate" but refused to get drawn into whether the poll findings were valid.