On his arrival, ElBaradei was asked by an Iranian journalist why he needed to visit when Iran had cooperated with the International Atomic Energy Agency (IAEA), to which he bluntly replied: "I think that does not necessarily reflect the facts."
"This is not a political issue, this is a technical issue," he added. He comment was an apparent dismissal of Iranian allegations that the IAEA was putting pressure on the Islamic republic because of lobbying by Tehran's arch-enemy, the United States.
The United States accuses Iran of using its atomic energy program as a cover for the secret development of nuclear weapons, a charge angrily denied by Tehran which insists it is only interested in producing electricity.
"I would like to close the issue tomorrow, if not today, but there are outstanding issues," ElBaradei said.
The IAEA director general told reporters accompanying him on his one-day visit that the 35-member board of governors of his Vienna-based anti-proliferation agency had become "impatient with Iran's cooperation".
The international probe into Iran's program "cannot go on forever. We have to discuss how to accelerate cooperation," he said. "We need to satisfy ourselves there are no undeclared nuclear activities in Iran."
ElBaradei said he "would like to make clear in my visit that restoring and accelerating cooperation is in the interests of everybody."
Later Tuesday was due to hold talks ElBaradei with President Mohammad Khatami, top national security official Hassan Rowhani -- the regime's point-man on the nuclear issue -- and the head of the national atomic energy body Gholam Reza Aghazadeh.
In a deal with the IAEA brokered by Britain, France and Germany in October last year, Iran agreed to make a full declaration of its nuclear activities, allow tougher IAEA inspections and suspend uranium enrichment-related activites.
But since then, inspectors have found undeclared designs for advanced P-2 centrifuges -- which can enrich uranium to weapons-grade -- and Iran also threatened to cut off cooperation altogether after such omissions from its declaration were condemned in Vienna.
In addition, Iran announced last week that it was resuming work at a uranium conversion facility in the central city of Isfahan, a key part of the sensitive nuclear fuel cycle that covers the early stages of uranium conversion before it is enriched.
Iran insists that does not violate its suspension, but the move has been criticised by the EU's big-three as likely to further damage confidence.
But an Iranian official greeting ElBaradei said he hoped the visit would manage to clear up the problems.
"We hope that all the outstanding issues will be sorted out, except the problem of contamination is a complicated problem," said Amir Hossein Zamani-Nia, director general at the Iranian foreign ministry for international political affairs.
A major question dogging the IAEA is how to account for traces of bomb-grade uranium found here. Iran says the traces came into the country on equipment bought on the black market from Pakistan, but the IAEA has yet to take samples in Pakistan to verify Iran's assertion.
"There are matters outside our control," Zamani-Nia told reporters. "But Iran has given all the information."
ElBaradei said earlier that no date had yet to be set for Pakistan -- a nuclear power -- to allow IAEA inspectors in to the country to carry out the so-called "environmental sampling" to compare certain key components with those sold on the international black market to Iran.
The next IAEA board meeting is in June, and Iran risks being declared in breach of the nuclear Non-Proliferation Treaty (NPT) and find its dossier on the desk of the UN Security Council -- which in turn could choose to impose punishing sanctions.
Zamani-Nia, however, said Iran was more optimistic.
"We hope that after the June meeting, the question of Iran will no longer be on the agenda of the IAEA board of governors," he said.