WASHINGTON—The Obama administration has concluded that uranium particles discovered last year at a secretive Iranian military base likely were tied to the country’s past, covert nuclear weapons program, current and former officials said, a finding that contradicts Tehran’s longstanding denials that it was pursuing a bomb.

Traces of man-made uranium were found at the Parchin facility, southeast of Tehran, by investigators from the International Atomic Energy Agency, the United Nations’ nuclear watchdog, as part of an investigation tied to the landmark nuclear deal reached last July between Iran and global powers.

The Iranians have claimed that the site was used for developing and testing conventional weapons. The particles were the first physical evidence—on top of satellite imagery and documents from defectors—to support the charge that Iran had been pursuing a bomb there.

The Obama administration didn’t comment about the uranium in December when the IAEA released its report; the finding got only one brief mention in the 16 pages. But in recent interviews, current and former U.S. officials asked about the uranium finding said the working assumption now is that it is tied to nuclear weapons development that Iran is believed to have pursued more than a decade ago.

“The existence of two particles of uranium there would be consistent with our understanding of the involvement of Parchin in a past weapons program, but by themselves don’t definitively prove anything,” said a senior administration official briefed on the evidence.