US military bombers carried out strikes against three Iranian nuclear facilities early Sunday local time using huge 'bunker-buster' bombs.
The results of the strikes are being closely watched to see how far they may have set back Iran's nuclear program.
The conference was aimed at disputing a leaked preliminary assessment from the US Defense Intelligence Agency suggesting the strikes may have only hampered Iran by months, counter to President Donald Trump's claim of 'total obliteration'.
It also gave Hegseth an opportunity to blast media that had reported the assessment.
Several experts have cautioned that Iran likely moved a stockpile of near weapons-grade highly enriched uranium out of the deeply buried Fordow site before the strikes, and could be hiding it in locations unknown to Israel, the US and UN nuclear inspectors.
They noted satellite imagery from Maxar Technologies showing "unusual activity" at Fordow on Thursday and Friday, with a long line of vehicles waiting outside an entrance to the facility.
A senior Iranian source told Reuters on Sunday most of the 60 per cent highly enriched uranium had been moved to an undisclosed location before the attack.
But Trump maintains it would have taken too long to remove anything.
"The cars and small trucks at the site were those of concrete workers trying to cover up the top of the shafts. Nothing was taken out of (the) facility," Trump wrote on his social media platform, without providing evidence.
The Financial Times, citing European intelligence assessments, reported that Iran's highly enriched uranium stockpile remains largely intact since it was not concentrated at Fordow.
Hegseth's said the Defense Intelligence Agency assessment was 'low confidence', and, citing comments from CIA Director John Ratcliffe, said it had been overtaken by intelligence showing Iran's nuclear program was severely damaged and would take years to rebuild.
Ratcliffe, Hegseth, Secretary of State Marco Rubio and General Dan Caine, the chairman of the Joint Chiefs of Staff, held a classified briefing on the strikes on Thursday for all 100 members of the US Senate.
Senators are expected to vote this week on a resolution that would require congressional approval for strikes against Iran, although the measure is not expected to be enacted.
At the Pentagon news conference, Hegseth described the strikes as "historically successful."
His comments came after Iranian Supreme Leader Ayatollah Ali Khamenei claimed victory in the 12 day war launched by Israel and vowed Iran would not surrender.
During the news conference, Hegseth criticised the media for having an anti-Trump bias.
"It's in your DNA and in your blood to cheer against Trump because you want him not to be successful so bad," Hegseth said.
"There are so many aspects of what our brave men and women did that ... because of the hatred of this press corps, are undermined," he said.
Trump praised Hegseth's news conference as: "One of the greatest, most professional, and most 'confirming' News Conferences I have ever seen!"
During the press conference, Caine, the top US general largely stuck to technical details, outlining the history of the bunker-busting bombs used. Caine showed a video testing the bombs on a bunker like the ones struck on Sunday.
Caine declined to provide his own assessment of the strike and deferred to the intelligence community. He denied being under any pressure to change his assessment to present a more optimistic view of the US strikes.
