Around 7,500 people from 15 different European countries were surveyed by the Commission.
They were presented with a list of 15 countries and asked to pick which ones represented a threat to world peace.
Some 59 per cent of respondents said they believed that Israel was a greater threat to world peace than North Korea and Iran.
Both North Korea and Iran have been declared pariah states by the US government, and were named as part of President Bush's 'axis of evil'.
The poll's findings will be released in full this Monday.
A right wing American Jewish thinktank has criticised the poll, calling it ''racist and a flight of fantasy''.
The group accused Europeans of falling foul of what it claims is an anti-Israel campaign orchestrated by ''European leaders and the media''.
The Simon Wiesenthal Centre has called for the European Union to be excluded from the quartet - US, Russia, and the UN - trying to broker a peace agreement between Israel and the Palestinians.
The centre's founder Rabbi Marvin Hier said that the findings of the survey showed that anti-Semitism is deeply embedded within European society, more than any other period since the end of the Second World War''.
Representatives from the centre will be meeting the Secretary General of the European Union, Javier Solana, later this month to discuss the results of the poll and issues around combating purported anti-Semitism in Europe.
The centre has launched a campaign to mobilise their members to bombard the European Commission with complaints about what they see as racism towards the state of Israel.
Pro-Israel campaigners often label as anti-Semitic any criticism of Israel or its policies.