The International Atomic Energy Agency (IAEA) says no deal has been reached on inspecting the Parchin site, south of Tehran, despite "intensive efforts".
The inspectors had sought to clarify the "possible military dimensions" of Iran's nuclear programme.
Iran insists it is purely for peaceful purposes, but the West suspects the programme has military implications.
The IAEA said that after two days of talks, its team was returning from Iran without a deal on a document "facilitating the clarification of unresolved issues" in connection with Tehran's nuclear programme.
The first round of discussions in January also failed to produce a result.
"It is disappointing that Iran did not accept our request to visit Parchin," IAEA Director General Yukiya Amano said in a statement.
It is suspected that Parchin was the site where explosives related to nuclear weapons may have been tested in recent years.
Israeli strike speculation
Meanwhile, Iran's envoy（使者） to the Vienna-based IAEA said Tehran expected to hold further talks with the agency.
Ali Asghar Soltanieh was quoted by Iran's Isna news agency as saying the latest discussions had been intensive and that talks would continue in the future.
The BBC's Bethany Bell in Vienna says the refusal to grant access to Parchin does not come as a major surprise, as there has been little progress in the negotiations between the two sides.
The inspectors' evaluation of their visits may form part of the next report on Iran's nuclear programme, expected later in February.
But last November, the IAEA said it had information suggesting Iran had carried out tests "relevant to the development of a nuclear explosive device".
This led to decisions by the US and the European Union to tighten sanctions against Tehran, including measures targeting the country's oil industry.
Tensions have risen further over speculation that Israel may carry out a military strike on Iran's nuclear facilities.
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