The letter comes one month after Barack Obama, the US president, warned the Arab world not to use the 150-nation IAEA forum to single out Israel.
Obama and Binyamin Netanyahu, the Israeli prime minister, agreed to work together
to oppose efforts to single out Israel at the upcoming IAEA conference.
At the time, Obama suggested that such a move would undermine the possibility of breakthrough talks on a Middle East nuclear-free zone, as proposed by the NPT conference three months ago.
But the Arab League letter says they were not attempting to single out Israel.
"Singling out a state assumes that there are a number of states in the same position and only one state was singled out," the letter says.
Referring to the NPT, the letter says: "The fact is that all the states in the region have acceded to the NPT except Israel."
Israel is commonly assumed to have nuclear weapons but refuses to discuss the issue.
Islamic nations have long called for Israel to open its programme for inspectors.
The Arab League's attempt to pressure Israel into unveiling its nuclear programme might deflect attention from Iran, which the United States and its allies accues of covertly seeking to build an atomic bomb.
Tehran denies the charge and insists its programme is for peaceful civilian purposes.