"There were certain criteria set for when the EU would leave the room and those criteria were not fulfilled," spokeswoman Cecilia Julin said.
The criteria agreed in New York before the Iranian leader spoke included denying the Holocaust and calling for the annihilation of Israel, which Ahmadinejad avoided doing this time.
Even so, a number of EU states did walk out when Ahmadinejad attacked Israel, including Britain, Denmark, France, Germany, Hungary and Italy.
"We're not commenting on who left or who didn't leave," Julin said. "I think there were other reasons for other countries that decided to leave."
In his address, Ahmadinejad again took aim at Israel but without mentioning the country or Jews by name, referring only to the "Zionist regime."
He accused Israel of "inhumane policies in Palestine," including genocide, and seeking to "establish a new form of slavery, and harm the reputation of other nations, even European nations and the US, to attain its racist ambitions."
Israel had called for a boycott of the speech, and was not present when the Iranian leader spoke. Canada heeded the boycott call, while delegations from Argentina, Australia, Costa Rica, New Zealand and the United States also left the room as Ahmadinejad began to rail against Israel, a European source said.