"It means that all the claims that Iran's nuclear activities have a military agenda and are deviant are not true. With the report the opposite has been shown to be true," chief nuclear negotiator Saeed Jalili told reporters.
He also said it showed that the referral of the nuclear file to the UN Security Council was wrong.
"For those who had doubts about the Iranian nuclear programme, the report is very clear and indicates that the basis upon which the nuclear case was referred to the Security Council has collapsed," he said.
He pointed to the agency's comments on Iran's uranium-enriching P1 and P2 centrifuges, which he said had undermined claims that the nuclear programme had military aims.
Iran has been hoping that its new cooperation with the International Atomic Energy Agency (IAEA) in clearing up outstanding questions over its nuclear drive will mean it avoids new UN sanctions.
Jalili slammed the actions of the Security Council, which has already imposed two sets of sanctions punishing Iran.
"This is useless in stopping the Iranian nation obtaining the rights that it is entitled to," he said.
"On what basis could they be looking to adopt a third resolution when Iran is cooperating with the agency and has answered its questions?" he added.
Jalili also warned that the cooperation with the IAEA would be affected if the Security Council went ahead and imposed a new sanctions resolution against Tehran.
"If they issue another resolution, which is unlikely, the implementation of the modalities of cooperation and the resolution of the issues will be affected," he said.
The report said that Iran has made some progress in revealing the nature and extent of its disputed nuclear programme, but needs to be more pro-active in providing information.