Clinton said the US and some of its allies were working on new measures to try and persuade Iran to change its course and reconsider its "dangerous policy decisions".
'Shift in rhetoric'
She also stressed that the administration of Barack Obama, the US president, wants a peaceful solution to the nuclear dispute, but she said that its patience would eventually reach a limit.
"I would like to figure out a way to handle it in as peaceful an approach as possible, and I certainly welcome any meaningful engagement, but ... we don't want to be engaging while they are building their bomb."
Asked what evidence the US had that Iran was pursuing nuclear weapons, PJ Crowley, the US state department spokesman, said that Washington was basing its assertions on Iran's actions.
"Given the current trajectory that Iran is on - the fact that it still has centrifuges spinning, and the fact that it is unwilling to constructively engage the international community - we have to assume that Iran is pursuing a nuclear programme," he told 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."
State Department spokesman on Clinton's comments about Iran's nuclear programme
Nazanine Moshiri, Al Jazeera's correspondent in the Iranian capital, Tehran, said Clinton's assertion of evidence of an Iranian nuclear weapon programme indicates a shift in US rhetoric.
"Most Iranians will be quite surprised by that because a few days ago the White House said Iran wasn't capable of reaching 20 per cent uranium enrichment," she said.
"Iran has told Al Jazeera they are capable of producing nuclear weapons but they are not going to. They only want to enrich to 20 per cent for their Tehran reactor."
Mahmoud Ahmadinejad, Iran's president, said on Thursday that the country's nuclear scientists had completed the further enrichment of the 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.
Iran has repeatedly stated that its nuclear programme is to meet the country's civilian energy needs.
Middle East peace
Clinton's comments at the forum, which is jointly organised by the Qatari foreign ministry and the US-based Brookings Institution, came only hours after she arrived in Doha for the start of a three-day visit to the region.
She is also using the trip to win Arab backing for the resumption of Israeli-Palestinian peace negotiations, a topic which she broached during her address.
"The goal of a comprehensive peace is fully in the interest of the United States. We are committed to our role in ensuring that negotiations begin and succeed," she said.
"Building a stronger relationship cannot happen overnight. It takes patience, persistence and hard work from all of us"
Hillary Clinton, US secretary of state
"I know that people are disappointed that we have not yet achieved a breakthrough. The president ... and I are disappointed as well.
"But we need to remember that neither the United States nor any country can force a solution. The parties must resolve their differences through negotiations."
Marwan Bishara, Al Jazeera's senior political analyst, said her remarks on the Israeli-Palestinian issue revealed nothing new about how the Obama administration would resolve the situation .
"There's an attempt to address the Palestine-Israeli question without putting any responsibility on the occupying force, Israel, " he said.
"We haven't heard much new there.
"But while there is a sense that the secretary of state asks everyone to take responsibility for their actions, there is no taking responsibility for the US failure to revive the deadlocked peace process by not fulfilling its pledge to end the dispute over Israeli settlements."
Clinton's speech comes eight months after a similar address by Obama, who called for a new beginning in ties between the US and the Muslim world during a speech in Egypt in June.
The secretary of state on Sunday addressed concerns that Obama's call during his speech was "insufficient and insincere".
"Building a stronger relationship cannot happen overnight. It takes patience, persistence and hard work from all of us," she said.
"We are and will remain committed to the president's vision for a new beginning."