Mohamed ElBaradei told Germany's Stern weekly that they were discovered on gas centrifuges at Natanz, 180 miles (290 kilometres) south of Tehran, where Iran is building a uranium processing plant.
"Natanz is the most critical point of our inspections. We took samples and found traces of highly enriched uranium," ElBaradei said.
"It is very worrying. If it emerges Iran is not using its nuclear programme for peaceful purposes, it could have terrible consequences."
He said Iranian authorities assured them the machinery involved was tainted before delivery to the site.
"We are checking that. Iran must lay everything open," ElBaradei added.
His remarks came as he prepared to present an assessment on Iran's nuclear programme to the board of governors of the International Atomic Energy Agency (IAEA) in Vienna.
Agency inspectors have visited Iran five times since June, taking numerous samples as well as receiving fresh information from Iranian authorities.
The IAEA has questioned whether uranium enrichment is needed for a civilian nuclear programme.
Tehran is under strong pressure from the international community to sign an additional protocol to the nuclear Non-Proliferation Treaty (NPT) which would allow IAEA inspectors to carry out surprise visits to its nuclear sites.
While the Islamic republic says that its nuclear programme is strictly for civilian purposes, the United States accuses it of secretly trying to develop nuclear weapons.
An IAEA spokesman said earlier Tuesday in Vienna that it remained concerned about Iran's nuclear programme and several issues needed "urgent" resolution.