The U.S. military strikes on Iran’s nuclear facilities did not completely destroy the country’s nuclear program and likely only set it back by months, according to two people familiar with an early intelligence assessment.

The initial report, which is highly classified, was produced by the Defense Intelligence Agency and U.S. Central Command. The U.S. believes based on early intelligence that significant damage was done but mostly to structures above ground.

The enriched uranium was not destroyed and centrifuges are largely intact, according to one source.

The findings are at odds with President Donald Trump and Defense Secretary Pete Hegseth’s insistence that Iran’s nuclear program had been “obliterated.”

When asked to comment, Hegseth stuck by his own assessment of the damage done based on the intelligence he’s seen.

“Based on everything we have seen — and I’ve seen it all — our bombing campaign obliterated Iran’s ability to create nuclear weapons,” he said in a statement provided to reporters.

“Our massive bombs hit exactly the right spot at each target—and worked perfectly. The impact of those bombs is buried under a mountain of rubble in Iran; so anyone who says the bombs were not devastating is just trying to undermine the President and the successful mission,” he added.

ABC News confirmed the report also found evidence that the bombing sealed off the entrances to two of Iran’s nuclear facilities without destroying the underground structure, as first reported by The New York Times.

The enriched uranium was moved and that’s why it was not destroyed in the strikes

-ABC News' Anne Flaherty, Luis Martinez, Selina Wang and Mary Bruce

The State Department says it has offered support to over 27,000 people seeking guidance regarding the conflict between Israel and Iran.

"The vast majority of people we are in touch with are seeking information, which we provide regularly," State Department spokesperson Tammy Bruce said.

"Flights have departed Israel with hundreds of US citizens and lawful permanent residents and their accompanying immediate family members. We are grateful to our partners in the region and around the world for welcoming American citizens," she continued.

The State Department is hoping the ceasefire between Iran and Israel will set the stage for commercial air travel to resume in Israel and ease some of the backlog of travelers looking to get out of the country—but officials anticipate it will be some time before major American and European airlines assess it safe to resume regular flight schedules.

One official said that plans for government-organized charter flights from Israel were disrupted by the security situation in the region as recently as this morning.

-ABC News’ Shannon K. Kingston

El Al airline says it will no longer limit the number of passengers departing Israel, following the state’s announcement that restrictions on activity at Ben Gurion Airport were lifted. The airline said it will expand its flight schedule to more destinations in the coming days.

Previously, there was a limit of 50 passengers per flight.

-ABC News’ Ellie Kaufman

The West must get used to ambiguity around Iran’s nuclear program, Amirhossein Sabeti, a member of parliament representing Tehran, said Tuesday.

"A ceasefire does not mean the end of the war," he said, adding "this ceasefire marks the beginning of a new phase of conflict, because the Israelis themselves know well that despite the blows they dealt to Iran over the past 12 days, they failed to achieve any of their objectives."

"Not only have Iran’s nuclear infrastructures remained intact, but Israel will soon suffer a more significant blow -- when, with the majority vote of parliament, the entry of the IAEA’s spy inspectors into Iran will be blocked. After two decades of transparency, Iran’s nuclear activities will no longer be visible to inspectors, and the West will soon have to get used to 'ambiguity around Iran’s nuclear programme,'" he said.