"Israel is not the only member state ... that has exercised its sovereign right not to accede to the NPT due to its national security considerations," Israel's Atomic Energy Commission chief Shaul Chorev said.
"Yet Israel is the only state that has been singled out, and is called upon to take a decision which is against its best national interests," he told the conference.
"Indeed, the advancement of states' accessions to international treaties does not fall within the mandate of the (IAEA)," he said.
The NPT, which came into force in 1970, has been signed by 189 states. Only three countries -- India, Pakistan and Israel -- have not signed it.
is among those that acceded to the treaty but violated it and withdrew in 2003.
The Jewish state is the only Middle East power believed to possess nuclear weapons.
Chorev said the resolution tabled by the Arab states was part of a "
to defame the state of Israel".
It was "incompatible with basic principles and norms of international law and does not fall within the mandate of the agency as defined in its statute," he said.
"Moreover, this resolution ... ignores the adverse reality in the Middle East region," Chorev said.
He said that Middle East states such as Iran, Syria, Libya and Iraq under Saddam Hussein -- all signatories to the NPT -- had "grossly violated their treaty obligations".
"These four cases make it absolutely clear that the NPT is unable to adequately address the security challenges in the Middle East region where the treaty has been most abused," Chorev said.
"The serious threat to the NPT and the non-proliferation regime is posed from within by those states that pursue nuclear weapons under the cover of their NPT membership."
The Arab states' resolution, which has been tabled every year for the past few years, is expected to be debated on Thursday.