The International Atomic Energy Agency (IAEA) has inspected the site once but has since been barred from returning.
"I would also ask Iran to support the agency's efforts to pursue further its investigation of the Lavizan-Shian and Parchin sites," Mohamed ElBaradei said on Tuesday, adding that his agency wanted to visit "areas of interest" at Parchin.
Parchin and Lavizan are among the sites where the United States suspects Iranian scientists have conducted research related to the development of nuclear weapons.
Iran says it has no interest in nuclear weapons, only in civilian nuclear technology to generate electricity.
ElBaradei, who was appointed for a third term on Monday as the head of the IAEA, said the agency was making progress in resolving one of two key outstanding questions about Iran's nuclear programme.
"Last month, the agency received from another member state a number of centrifuge components, on which we have been conducting environmental sampling," ElBaradei said in the written text of his speech to the IAEA board of governors.
The "member state" in question is Pakistan, IAEA officials say.
The father of Pakistan's atom bomb, Abdul Qadeer Khan, sold Iran centrifuges, machines used to purify uranium to fuel power plants or weapons, on a global black market that also supplied Libya and possibly North Korea.
A preliminary analysis of Pakistani components for enrichment centrifuges identical to ones Iran purchased from Pakistan appears to back Tehran's assertion that the traces of bomb-grade uranium were the result of contamination, Vienna officials familiar with the IAEA investigation of Iran said.
ElBaradei chided Iran for not providing the IAEA full documentation of its centrifuge programme, the second major outstanding issue the agency has been unable to resolve.
"We have continued to press for additional documentation regarding offers of equipment made to Iran," ElBaradei said, adding that what Iran has provided is "not yet sufficient".