Israel is widely believed to be the Middle East's sole nuclear arms possessor with up to 300 warheads, but it has long refused to confirm or deny it has such weapons and unlike Iran is not a signatory to the Non-Proliferation Treaty.
"Silence and negligence about Israel's nuclear programme sends a negative message to the NPT members," Kazem Gharibabadi, Iran's ambassador to the UN agency, tweeted.
Being an NPT signatory meant "accepting the robust verifications", while being outside it meant being "free from any obligation and criticism, and even (getting) rewarded", he wrote.
"What is the advantage of being both a NPT member and fully implementing the agency's safeguards?
Gharibabadi was reacting to an interview given by IAEA Director General Rafael Grossi to Energy Intelligence earlier this month.
Asked why the IAEA is so focused on Iran's nuclear programme but not Israel's, he responded: "Our relation with Israel is based on the one that you have with a country which is not a party to the NPT."
Iran has been a signatory to the NPT since 1970, the year it came into force, and has always denied it has any ambitions to acquire or manufacture an atomic bomb.
Israel, which has never signed up to the treaty, has repeatedly warned that it will do whatever it takes to prevent Iran obtaining nuclear weapons.
The NPT calls on nations "to achieve the cessation of the nuclear arms race and to undertake measures in the direction of nuclear disarmament".
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