Mr El Baradei will step down at the end of 2009
The IAEA chief has reacted sharply to an Israeli accusation of bias in his attitude toward Syria, in a rare public controversy at the nuclear watchdog.
The body has been examining the case of an alleged Syrian nuclear arms facility that Israeli jets bombed in 2007.
Israel's envoy told an IAEA debate on the subject in Vienna that Mohamed ElBaradei must "avoid political bias".
Mr ElBaradei, an Egyptian, accused Israel of breaking international law and said "stop preaching to us".
Mr ElBaradei said Israel's attack on the facility had hampered his attempts to unearth the truth about the site.
Details of IAEA meetings rarely reach the public domain and open criticism of the head of a UN body such as Mr ElBaradei is almost unheard-of, correspondents say.
Syria became subject to IAEA investigation in 2007 after Israel jets destroyed what the US said was a nearly finished nuclear reactor, built with North Korean help, that could produce plutonium, a substance used in nuclear warheads.
Syria denies the accusations, but after allowing International Atomic Energy Agency inspectors in 2008, it repeatedly blocked requests for further access.
During the first visit, the IAEA investigators found uranium traces at the site.
Syria said it was a result of Israeli weaponry used in the air strike.
Tension boiled over at the meeting when Israel's envoy, Ambassador Israel Michaeli, accused Mr ElBaradei of making repeated, "redundant" demands for more information.
"Israel has responded timely and in good faith to the question addressed to it regarding the possible origin on the uranium particles, traced in the site of the nuclear reactor in Deir al-Zour," Mr Michaeli said.
"Had the director-general wished for further information from Israel, he would have not refused to meet with Israeli officials, and refrained from publicly lashing at Israel.
"Israel calls on the director general to avoid political bias in dealing with the Syrian file," Mr Michaeli concluded in a transcript made available to the media.
Mr ElBaradei was quick to respond saying: "When Israel bombed what was claimed to be a nuclear facility, it was not only hampering our work, but it was a clear violation of international law.
"You, sir, your action is deplored by not allowing us to do what we're supposed to do under international law. You're not even a member of the (NPT) regime to tell us what to do. We would appreciate it if you stopped preaching to us."
He added that given what he characterised as Israel's scant regard for the work of the IAEA, "I'll not dignify (the charge) that we're biased".
Separately, he did also admonish Syria for blocking access to the site and withholding documentation.
The US deputy chief of mission also waded into the heated discussion at the IAEA headquarters in Vienna, accusing Syria of being obstructive.
"Regrettably, Syria has not used this time to resolve the lingering questions about the reactor and the associated facilities... Instead, the agency's list of questions is growing," said Geoffrey Pyatt.