"The more we report and the more we see, the more we understand how devastating those attacks were on all three of those nuclear sites," Hegseth told Pentagon pool reporters on Friday.
US attacks on June 22 hit Iran's nuclear sites of Fordow, Esfahan and Natanz.
Hegseth's remarks come after a report by NBC News on Thursday citing current and former US officials saying just one of the three nuclear facilities struck by the US in Iran last month has been destroyed.
That assessment, which showed that Fordow was set back as long as two years, was briefed to US lawmakers, Defense Department officials and allied countries in recent days.
An initial Pentagon assessment suggested the attacks had only set Iran's nuclear program back by months, but subsequent analysis released by the Central Intelligence Agency said it would take Tehran years to recover.
Trump on Wednesday said Iran's nuclear program had been dealt an irreparable blow by the US attacks and that he was in no rush to resume negotiations with Tehran despite its alleged eagerness.