Tehran has repeatedly stated that its nuclear programme is purely to meet the country's civilian energy needs.
Mohammad Marandi, a political analyst at the University of Tehran, dismissed Clinton's comments.
"If we give Hillary Clinton some more time she will be blaming Iran for global warming as well," he told Al Jazeera.
Watch Hillary Clinton's Middle East Town Hall meeting on Al Jazeera:
Tuesday at 1900 GMT, Wednesday at 0300 and 1400 GMT, and on Thursday at 0600 GMT.
"Obviously the statements that she has been making over the past couple of days are quite dishonest, the fact is the United States has to deal with Iran on a rational basis otherwise it will get itself nowhere."
The comments by the US secretary of state marked a stepping up of pressure in favour of sanctions on Iran.
The US is hoping to use international pressure through the UN Security Council for a fourth round of sanctions on Iran.
Clinton said that those sanctions would expressly target the business interests of Iran's Revolutionary Guard.
However, she said that Washington was not planning military action against Iran.
"We are planning to try to bring the world community together in applying pressure to Iran through sanctions adopted by the United Nations that will be particularly aimed at those enterprises controlled by the Revolutionary Guard, which we believe is, in effect, supplanting the government of Iran."
Her comments came a day after she told delegates at the US-Islamic World Forum, also in Qatar, that Iran had left the world powers little choice but to impose harsh penalties against it over its nuclear programme.
Clinton told the forum, which is jointly organised by the Qatari foreign ministry and the US-based Brookings Institution, that "evidence is accumulating" that Iran is trying to build a nuclear weapon.
"Iran has consistently failed to live up to its responsibilities. It has refused to demonstrate to the international community that its nuclear programme is entirely peaceful," she said.
PJ Crowley, the US state department spokesman, later echoed that sentiment in an interview with Al Jazeera.
"Given all the steps that Iran has taken and all the actions that Iran refuses to take, we can only begin to draw the conclusion that Iran's intentions are less than peaceful," he said.
Mahmoud Ahmadinejad, Iran's president, said last week that his country's nuclear scientists had completed further enrichment of the first batch of its stockpile of uranium.
Tehran has said that it stepped up enrichment to produce fuel for a medical research reactor, but the US and its allies have said that the move signals a rejection of a UN-backed plan to swap Iran's low-enriched uranium for processed nuclear fuel.
Clinton flew to Saudi Arabia after Qatar in a further attempt to secure support for action against Iran.
US officials have suggested that Riyadh could help the situation diplomatically by offering China guarantees it would meet Beijing's oil requirements, possibly easing its reluctance to impose further sanctions on Iran.