"The agency assesses that a range of activities relevant to the development of a nuclear explosive device were conducted in Iran prior to the end of 2003 as a coordinated effort, and some activities took place after 2003," the International Atomic Energy Agency said.
It said however that "these activities did not advance beyond feasibility and scientific studies, and the acquisition of certain relevant technical competences and capabilities."
It added: "The agency has no credible indications of activities in Iran relevant to the development of a nuclear explosive device after 2009."
In July, Iran and major powers agreed a landmark deal downscaling its civilian nuclear programme.
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As part of that accord, Iran also undertook to engage more with the IAEA in order to clear up the allegations, which Tehran has always rejected.
Iran has warned that it will not implement key parts of the July deal with major powers unless the PMD file is "closed".
The IAEA board is due to meet on December 15 to discuss the new report.