But the global agreement in 2015 makes no distinction between military and non-military sites, said Haley after she returned from a trip to the IAEA headquarters in Vienna. Even before assuming office, Trump has lashed out at the nuclear deal, describing it as the "worst deal ever negotiated".
The shaky nuclear deal agreed between Iran and six world powers in July 2015 endured another jab on Thursday, as Iran threatened to renege on its commitments.
At the meeting, she spoke with IAEA Director-General Yukiya Amano in order to enhance the Trump administration's understanding of Iran's compliance with the nuclear agreement and ask questions about the military dimensions of Iran's nuclear facilities.
"There were already issues in those locations, so are they including that in what they look at to make sure that those issues no longer remain?"
In her official statement following her meeting with Amano on Wednesday, Haley did not mention "military sites" specifically.More news: Chow Yun-fat helps to clean up HK streets after Typhoon Hato
After years of tension with the West, Iran struck a deal with the five world powers of Britain, China, France, Germany, Russia and the United States in July 2015 on a comprehensive deal, under which Iran agreed to limit its uranium-enrichment activities in return for the lifting of western and worldwide sanctions.
Washington wants to know if the IAEA plans to inspect Iranian military sites during its verification of Tehran's compliance with the JCPOA.
Iran's top authorities have rejected giving global inspectors access to their military sites and officials have told Reuters any such move would trigger harsh consequences. "Hopefully visiting the IAEA will allay concerns about monitoring the agreement and demonstrate to Haley that the deal put Iran's nuclear program under a microscope and keeping it there is the best way to guard against any illicit nuclear activity", she said.
Haley's trip to the IAEA was a part of that process.
"Why would they say that if they had nothing to hide?" We have not achieved the deal easily to let it go easily.More news: 'The Batman': Everything You Need To Know About The DC Film
The Trump administration has twice certified Iran's compliance with the deal.
Earlier, Iranian Foreign Minister Mohammad Javad Zarif wrote in a letter to the IAEA that Haley's visit undermined "the independence and credibility" of the inspectors and warned the IAEA not to share extra information about the regime's nuclear program.
On Tuesday, Iran's nuclear chief, Ali Akbar Salehi, warned that Iran could "resume 20-percent enrichment in, at most five days".
Separately on Wednesday, Zarif said in an interview that the IAEA "should not allow questions to be raised about its independence and status in connection with the JCPOA in the global arena".
Haley also leveled harsh criticism at Irish Major General Michael Beary, the commander of United Nations forces in Lebanon, accusing him of turning a blind eye to Iran's alleged covert arming of the Hezbollah resistance group.More news: In Kiev, Mattis says Moscow wants to redraw borders by force
One issue that Haley is pursuing at the U.N.is the interpretation of the nuclear agreement, and whether launching ballistic missiles is in violation of its terms.