"We think that Honduras has taken important and necessary steps that deserve the recognition and the normalisation of relations," she told a news conference on Thursday, on the sidelines of a meeting of regional officials in Costa Rica.
Clinton also praised Porfirio Lobo, the new Honduran president elected in November, for taking steps to resolve the political crisis triggered by Zelaya's removal.
But countries such as Argentina and Brazil are balking at restoring ties with Honduras, calling instead for Zelaya to be restored to power.
|Manuel Zelaya says his proposed constitutional amendments were to help the poor [AFP]
They believe restoring diplomatic ties with Honduras now would reward the coup leaders who ran an interim government until January.
Clinton, who made the case for Honduras while visiting the two countries, said Lobo and the new administration "have taken the steps necessary to restore democracy" and reconcile the population split over the coup.
"We share the condemnation of the coup that occurred, but we think it is time to move forward and ensure that such disruptions of democracy do not and cannot happen in the future," she said.
Zelaya, a leftist populist, was forced from power by the military on June 28, the same day he planned to hold a non-binding referendum on changes to the constitution that would have allowed him to run for re-election.
The supreme court in Honduras and congress had opposed the public vote, saying Zelaya was trying to win support to allow presidents to serve more than a single term.
Zelaya, currently in exile in the Dominican Republic, has denied the claims saying that the constitutional changes he sought were aimed at improving the lives of the poor.