The IAEA also took "strong exception" to claims made over the removal of a senior safeguards inspector.
There was no immediate comment from Washington over the letter.
But Rep Rush Holt, a Democratic member of the House intelligence committee, which released the report, said it had never been meant for release to the public.
"This report was not ready for prime time and it was not prepared in a way that we can rely on. It relied heavily on unclassified testimony," he told the BBC's PM programme.
'Deja vu'
Signed by a senior director at the International Atomic Energy Agency, Vilmos Cserveny, the letter raises objections over the committee's report released on 23 August.
It says the report was wrong to say that Iran had enriched uranium to weapons-grade level when the IAEA had only found small quantities of enrichment at far lower levels.
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The letter took "strong exception to the incorrect and misleading assertion" that the IAEA removed senior safeguards inspector Chris Charlier for "allegedly raising concerns about Iranian deception" over its programme.
It said Mr Charlier had been removed at the request of Tehran, which has the right to make such an objection under agreed rules between the agency and all states.
He remains head of a section investigating Iran, the IAEA says.
The letter went on to brand "outrageous and dishonest" a suggestion in the report that he was removed for not adhering "to an unstated IAEA policy barring IAEA officials from telling the whole truth" about Iran.
The letter, sent to Peter Hoekstra, head of the House of Representatives' Select Committee on Intelligence, was aimed at setting "the record straight on the facts", the IAEA said.
"This is a matter of the integrity of the IAEA and its inspectors," spokeswoman Melissa Fleming said in a statement.
A Western diplomat called it "deja vu of the pre-Iraq war period".
The IAEA and the US clashed over intelligence that Saddam Hussein had weapons of mass destruction in the lead-up to the war in Iraq in March 2003.