"We will use many means to try to disrupt these programs," Rice told NBC television. "The president will look at all the tools that are available to us."
Rice was asked about a New York Times report that quoted unnamed senior US officials as saying they were seeking to step up covert actions against Iran "to disrupt or delay as long as we can" Tehran's nuclear weapons drive.
"We are having diplomatic successes, but these are very tough problems," Rice said.
"For a long time ... we were the only who ones who seemed to think that Iran really did have an aggressive program to try to develop nuclear weapons," she said.
"We are now getting stronger (International Atomic Energy Agency) action against them. We believe in September we will get a very strong statement out of the (IAEA) board that Iran will either be isolated or it will submit to the will of the international community."
US Secretary of State Colin Powell said last month that it was "more and more likely" that Iran would be referred to the UN Security Council by the IAEA as a possible prelude to sanctions.
The United States has accused Iran of wantonly flouting international calls to curb its nuclear activities, saying Tehran is engaged in a "direct challenge" to the UN's nuclear watchdog.
The European Union's "big three" -- Britain, France and Germany -- have been pressing Iran to cease working on the nuclear fuel cycle in exchange for increased trade and cooperation and the guaranteed supply of nuclear fuel from abroad.
Such work is permitted under the nuclear Non-Proliferation Treaty (NPT), but fears persist that once fully mastered, a country possessing such technology can easily divert it into military usage.
Many diplomats believe that even if Iran is not working on nuclear weapons now, it would like to have the option in the future. Tehran, meanwhile, denies charges it is seeking to develop a nuclear bomb.
Iran has agreed to temporarily suspend enrichment pending the completion of an International Atomic Energy Agency (IAEA) probe, but is working on other parts of the fuel cycle and has recently resumed making centrifuges used for enrichment.