A spokesman for Iran's UN Mission said the weapons "are absolutely and under no condition negotiable".
His denial comes after Foreign Minister Mohammad Javad Zarif suggested in an interview that the missiles could be up for discussion if sanctions are lifted, reported the BBC.
The US unilaterally withdrew from a landmark 2015 nuclear deal last year and reimposed tight restrictions.
In response, Iran announced in July it has surpassed limits on enriched uranium imposed in the agreement. The country insists it is not trying to build nuclear weapons.
In a television interview on Monday, Zarif told broadcaster NBC News that "room for negotiation is wide open" once the US removed its punishing sanctions.
Asked if this would include discussions about Iran's missiles - something absent from the original 2015 agreement - Iran's Foreign Minister said if the US wanted to discuss the programme "they need, first, to stop selling all these weapons, including missiles, to our region".
But Alireza Miryousefi, a spokesman for Iran's UN Mission, said Iran "categorically rejects" the "characterization" of their Foreign Minister's interview, and attacked media reports of his words.
"Drawing a false conclusion in pursuit of headlines, when what was said in the context was obvious, only leads to a diminution of the standing of the press with the public," he tweeted.
At a cabinet meeting on Tuesday, US Secretary of State Mike Pompeo said Iran had "for the first time" shown its willingness to discuss the weaponry. The country has previously insisted this was not an option under any circumstances.
US President Donald Trump said the US had made "a lot of progress" with Iran and that they were "not looking for regime change", although he insisted the country cannot develop a nuclear weapon and "can't be testing ballistic missiles".
Meanwhile, the President's nominee for Defence Secretary, Mark Esper, told the Senate Armed Services Committee on Tuesday the US is not looking for war with Iran and needs to "get back on the diplomatic channel".
( With inputs from IANS )