Ali Asghar Soltanieh said that Iran's uranium enrichment programme, which Western powers have raised concerns over, was a separate issue to the deal.
When asked if Iran would continue enriching uranium to higher levels if the deal went through, he said: "This is not the issue."
Confirming the receipt of Iran's letter, Ban Ki-moon, the UN secretary-general, said: "If accepted and implemented, it could serve as an important confidence-building measure and open the door for a negotiated solution to the Iranian nuclear issue".
He said Iran "should show greater transparency about its nuclear programme" and stressed the "importance of Iran's full co-operation with the IAEA and full compliance with relevant Security Council resolutions".
The IAEA said it would pass on Iran's letter to the US, France and Russia, part of the so-called Vienna Group, but did not comment on the deal.
Iranian diplomats travelled to the residence of Yukiya Amano, the IAEA chief, in Vienna, Austria along with representatives from Turkey and Brazil, for a 45-minute meeting on Monday.
Jonah Hull, Al Jazeera's correspondent in Vienna, said the letter was handed over as the discussion took place behind closed doors at the residence.
"The letter included details of the deal and details of Iran's commitment," he said.
"In terms of the deal we don't yet have chapter and verse on this letter ... but we understand this is a deal to swap nuclear fuel."
Iran signed a deal last week with Brazil and Turkey, non-permanent members of the UN Security Council, to ship over half of its low-enriched uranium abroad in exchange for fuel for a Tehran medical research reactor.
Under the plan, Iran would transfer 1,200 kg of low-enriched uranium (LEU), which is enough for an atomic bomb if enriched to high purity, to Turkey in return for special fuel rods to replenish the stocks of its medical isotope reactor.
But Western governments have been dismissive of the proposal, which they have said fails to address international concerns about Iran's nuclear programme.
They have said that since Iran's LEU stockpile has grown significantly since the proposal was first raised seven months ago, meaning it could still be left with enough for a nuclear warhead.
US pressing ahead
Western powers believe the Islamic state wants highly enriched uranium to make an atomic weapon, but Tehran says its programme is simply designed to meet its civilian energy needs.
Washington has pressed ahead with circulating a new sanctions resolution.
PJ Crowley, US assistant secretary of state for public affairs, said that Washington was reviewing a copy of the letter received from the IAEA.
"As we have said, we remain concerned about Iran's defiance of Security Council resolutions, its ongoing enrichment activity and failure to meaningfully engage the P5+1," he said.
"Nothing in the letter changes these broader concerns."
Anita McNaught, Al Jazeera's correspondent in Istanbul, said: "Turkey and Brazil have stood steadfastly by Iran in this, and the most positive sounds coming out today are from Turkey who say they stand by the deal.
"Turkey’s view is very simple: sanctions have been tried in the past and they haven’t worked. They are determined to make their case in every international arena possible.
"They say this deal should be given a chance to be worked through."
An original deal brokered between Iran, the US, France and Russia in October last year foundered in disputes over detail.
Iran had previously been reluctant to allow its stockpile of uranium to leave the country before receiving the nuclear fuel, saying that the exchange must take place simultaneously inside the country.