It said Iran had told the UN agency the presence of traces of highly refined uranium - at a level that could take it further down the road to potential weapons-grade threshold - "may happen for technical reasons beyond" its control.
"The Agency is assessing Iran's explanation and has requested further details," the International Atomic Energy Agency (IAEA) report said.
The United States - which like its Western allies and Israel accuse Iran of seeking to develop nuclear arms capability - said the Iranian explanation could be accurate.
"There are a number of possible explanations for this, including the one that the Iranians have provided," State Department spokeswoman Victoria Nuland said in Washington.
"We are going to depend on the IAEA to get to the bottom of it."
Enriched uranium can be used to fuel power plants, which is Iran's stated purpose, or provide material for bombs, if refined to a much higher degree, which the West suspects may be Iran's ultimate goal. The Islamic Republic denies that.
The IAEA report said environmental samples taken in February at Iran's Fordow facility - buried deep beneath rock and soil to protect it from air strikes - showed the presence of particles with enrichment levels of up to 27 percent.
That is above the 20 percent enrichment level Iran has declared at the site, and takes it across the line from low-enriched to high-enriched uranium.
It is "significantly" above the threshold level, one diplomat familiar with the issue said, adding a "number" of such particles had been discovered. Further samples were taken earlier this month to see whether the discovery was confirmed.
US proliferation expert David Albright said he believed it was a production glitch that caused the trace at Fordow. Nevertheless, it is "embarrassing for Iran."
The IAEA report suggested it is possible that particles of uranium enriched to higher-than-declared levels may be the result of a technical phenomenon associated with the start-up of centrifuge cascade.
The quarterly IAEA report was issued to member states a day after six world powers - the United States, Russia, Britain, Germany, China and France - failed to convince Iran to halt its 20 percent enrichment during a May 23-24 meeting in Baghdad.
Iran started enriching to this level in 2010 and has since sharply expanded the activity, saying the material will serve as fuel for a medical reactor. But a suspicious West is alarmed since such enhanced enrichment accomplishes much of the technical leap towards 90 percent - or weapons-grade - uranium.
Iran has increased its stockpile of 20 percent uranium to around 145 kg in May from nearly 110 kg some three months ago, the report said. Western experts say about 250 kg is needed for a nuclear bomb, if processed further.
The report also showed Iran had installed 368 enrichment centrifuges at Fordow facility in addition to the 696 already operating there.
Although not yet being fed with uranium, the new machines could be used to further expand Iran's output of uranium enriched to a fissile concentration of 20 percent, the part of the country's nuclear programme that most worries the West.
The UN agency also said satellite images showed "extensive activities" at the Parchin military complex, southeast of Tehran, which inspectors want to check over suspicions that nuclear weapons-relevant research was done there.
The "activities" could hamper the IAEA's inquiry, it said - an allusion to what Western diplomats have said may be Iranian efforts to remove incriminating evidence. Iran has denied pursuing a clear weapons capability there or anywhere else.
The UN watchdog told Iran in a letter sent this month that it needed "early access" to Parchin, the report said. Iran has repeatedly refused this, maintaining that Parchin is a solely conventional military base.
The IAEA said it had urged Iran to expedite a final agreement to enable inspectors to resume their long-running investigation into suspected nuclear explosive experiments.
IAEA chief Yukiya Amano had said earlier this week after talks in Tehran that the two sides were close to such a deal although "some differences" remained before it could be sealed.