IAEA head Mohamed ElBaradei said Iran's stonewalling of his agency was a "serious concern."
"Iran needs to give the agency substantive information" to clear up suspicions, he said at the start of a 35-nation board IAEA meeting, in comments made available to reporters.
Diplomats at the gathering described ElBaradei's comments as unusually blunt.
ElBaradei rejected the Iranian suggestion that the IAEA probe could expose non-nuclear military secrets, saying the IAEA "does not in any way seek to 'pry' into Iran's conventional or missile-related military activities."
"We need, however, to make use of all relevant information to be able to confirm that no nuclear material is being used for nuclear weapons purposes," he said, urging Iran to "implement all measures required to build confidence in the exclusively peaceful nature of its nuclear program at the earliest possible date."
If Tehran fails to do so, the IAEA "will not be able to provide credible assurances about the absence of undeclared nuclear material and activities in Iran," he said.
A senior Iranian envoy accused the United States of trying to use the IAEA as a tool in Washington's confrontation with Tehran. Iran, he said, has demonstrated full cooperation with the agency. Allegations of nuclear weapons work by Tehran is based on forged documents and the issue is closed, the envoy said.
With time running out before Tehran develops potential nuclear weapons capacity, some worry that Israel or the U.S. might resort to military strikes if they believe all diplomatic options have been exhausted.
And with Tehran showing no signs of giving up uranium enrichment or heeding other international demands, the diplomatic window appears to be closing.
Outside the meeting, an indignant Ali Ashgar Soltanieh, the chief Iranian delegate to the IAEA, rejected suggestions his country was hiding something, and accused Washington of hijacking the agency for an anti-Iran campaign.
"The international community and all member states of the IAEA are frustrated with this kind of United States actions in the IAEA," he told reporters. "The Americans are every day isolating themselves.
"Iran is of course very advanced in missile activities and technology," he said. "But there is no activity at all related to nuclear weapons."
Ahead of the meeting, hard-line Iranian President Mahmoud Ahmadinejad declared that Iran's military will "break the hand" of anyone targeting the country's nuclear facilities.
Iran insists its nuclear activities are geared only toward generating power. But Israel says the Islamic Republic could have enough nuclear material to make its first bomb within a year. The U.S. estimates Tehran is at least two years away from that stage.
Physicist and former U.N. nuclear inspector David Albright says says Tehran could reach weapons capacity in as little as 6 months through uranium enrichment.
An IAEA report drawn up for the IAEA board meeting says that Tehran has increased the number of centrifuges used to process uranium to nearly 4,000 from 3,000 just a few months ago.
But Albright, whose Washington-based Institute for Science and International Security closely tracks suspect secret proliferators, says he has also been able to extrapolate other information from the report that is less obvious but of at least equal concern.
Iran, he says, has managed to iron out most of the bugs in the intensely complicated process of enrichment that often saw the centrifuges breaking down. The machines, he says "now appear to be running at approximately 85 percent of their stated target capacity, a significant increase over previous rates."
That, he says means, they can produce more enriched uranium faster. And while the IAEA says that the machines have spewed out only low-enriched material suitable solely for nuclear fuel, producing enough of that can make it easy to "break out" quickly by reprocessing it to weapons- grade uranium suitable for the fissile core of a warhead.
To date, Iran has produced nearly 1,000 pounds of low-enriched uranium, said the report - close to what Albright says is the 1,500-pound minimum needed to produce the 45-60 pounds needed for a simple nuclear bomb under optimal conditions.
And with Iran's centrifuges running ever more smoothly, it "is progressing toward this capability and can be expected to reach it in six months to two years," says Albright.
Additional work - making a crude bomb to contain the uranium - would take no more than a "several months," he said.
But that work could be done secretly and consecutively with the last stages of weapons-grade enrichment. With Iran limiting access of IAEA inspectors to facilities it has declared to the agency, the U.N. nuclear monitor is blind-sided in efforts to establish whether such covert atomic work is going on.
By Associated Press Writer George Jahn