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The meeting was the latest attempt by the UN agency to access Iran's nuclear sites and interview its scientists about what many believe is an undercover nuclear weapons program.
Iran and the International Atomic Energy Agency (IAEA) failed to reach an agreement this week over the former's nuclear program.
"We had discussions on the structured approach document but could not finalize the document," said Herman Nackaerts of the International Atomic Energy Agency after returning from Tehran, reported Reuters.
"Our commitment to continued dialogue is unwavering. We will work hard now to resolve the remaining differences but time is needed to reflect on the way forward. We haven't agreed yet on a date for the next meeting."
ChannelNewsAsia said the meeting was the latest attempt by the agency to access Iran's nuclear sites and interview its scientists.
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Western countries and the IAEA have accused Iran of working on an undercover nuclear weapons program. Iran continues to deny the allegations.
The separate IAEA talks come just weeks before scheduled meetings between Iran and the UN Security Council members with Germany in Kazakhstan.
Iran walked away from the last so-called P5+1 talks after members refused to lift sanctions against the country that were put in place last year.
After the recent IAEA talks, Iran's envoy was far more upbeat than his UN counterpart, reported AAP.
"Some differences were resolved and agreement on some issues in the modality was reached," Ali Asghar Soltanieh said to Iranian reporters, reported ChannelNewsAsia.