Micheletti's early exit from the mediated talks came after he met Arias in a closed-door meeting at the Costa Rican president's private residence.
Zelaya held a separate two-hour private meeting with Arias earlier in the day after the Honduran rivals refused to meet each other.
Arias, a Nobel peace laureate, is serving as the main mediator between Zelaya and the interim Honduran government after attempts by the Organisation of American States (OAS) and the United Nations to solve the crisis failed.
The premature exit of Micheletti from the mediated talks is "one of the worst-case scenarios" for the negotiations, our correspondent said.
"What people were looking for, both in Honduras and among the international community, was some kind of definitive solution," he said, adding that this was probably going to lead to more uncertainty.
Zelaya told Al Jazeera on Wednesday that he was confident that the country's military-backed interim government would be dismantled as a result of the talks.
He said that he was seeking the resignation of the coup leaders who had forced him into exile, arguing that international opinion was on his side.
"What is going to be done is to fulfil the resolution of the Organisation of American States and the resolution of the United Nations, in which they ask first and foremost for the reinstatement of the president of the republic," he said.
"Number two is the complete non-recognition of the authorities by coup d'etat, and condemnation of the coup d'etat."
But while Zelaya has demanded that he be swiftly reinstated as president, the interim government has maintained a tough line against him.
"This isn't a situation that can be resolved in a blink of an eye," Carlos Lopez, designated by Micheletti's interim government as envoy to the UN, said in Tegucigalpa, the Honduran capital.
Lopez reiterated the interim government's assertion that the Zelaya would face charges if he returned to Honduras.
Speaking to Al Jazeera on Wednesday, Antonio Rivera Callejas, a senator in the Honduran congress and a minority leader of the opposition National Party of Honduras, maintained that "what happened in Honduras was not a military coup - it was constitutional".
"The supreme court, the 15 judges, by a unanimous decision, [ruled] that Zelaya was violating the laws in our constitution. Then the congress acted.
"The president was taken out of our country for his own safety. If he had stayed here, blood would have been on the streets."
Callejas added that "if Zelaya wants to come back, he is welcome, but he will be judged by all citizens".
US suspends aid
Meanwhile, after nearly two weeks of mostly muted response from the US, Washington said on Wednesday that it had suspended $16.5m in military assistance programmes and development assistance programmes to the Honduran interim government.
About $50m more in assistance "could be in jeopardy" this year alone, it said.
But the US government said that "programmes that directly benefit the Honduran people are continuing", including "supporting the provision of food aid, HIV/Aids and other disease prevention, child survival, and disaster assistance, as well as election assistance to facilitate free and fair elections".
Zelaya was removed from power on June 28 as he was about to press ahead with a non-binding referendum on the constitution.
His domestic critics said the public vote was aimed at changing the constitution to enable him to run again for office at the end of his current four-year term.
Zelaya attempted to return to Tegucigalpa, the Honduran capital, on Sunday but soldiers and military vehicles blocked the runway and warned off his aircraft.
At least one person among the thousands of people waiting for the plane to land was killed by security forces - the first to die in clashes since the coup.