Ahmadinejad caused outrage in the West and Israel for saying in 2005 the state of Israel should be wiped off the map and for a Tehran conference in 2006 that sought to cast doubt on the Holocaust, in which 6 million Jews were deliberately killed by the Nazis.
The Islamic Republic does not recognize Israel's right to exist and refers to it as the "Zionist regime". It has condemned Israel's recent attacks in Gaza, which Ahmadinejad has described as "genocide".
At Tuesday's conference he said in a message read out by the government spokesman that "the illegitimate Zionist regime is one of the consequences of the Holocaust," state broadcaster IRIB reported on its website.
"Breaking the lock on the Holocaust box and opening it is tantamount to cutting the Zionist regime's life jugular and the bulk of the [Zionist] philosophy would collapse," said his message to the conference at Sharif Technical University.
Iranian media did not give details on who organized the conference or who attended it.
Ahmadinejad, who often rails against Israel and the West, said the subject of the Holocaust had been used to expand the international influence of the United States and Britain after World War Two, IRIB reported.
He said "power-seeking networks introduced themselves as defenders of a number of victims and issued an order that the survivors ... must receive blood money, part of which was the establishment of the Zionist regime on Palestinian territory."
Last September, President Shimon Peres called Ahmadinejad a danger and a disgrace at the United Nations, after the Iranian president blamed "Zionist murderers" for everything from the Wall Street crisis to Russia's invasion of Georgia.
Israel, believed to have the Middle East's only atomic arsenal, and the West say Iran has a covert programme to build nuclear weapons. Iran, the world's fourth largest oil producer, denies this, saying it wants technology to generate electricity.
Peres has called Iran's nuclear program an "existential threat" to Israel.