Zelaya then left Costa Rica, heading to Guatemala and the Dominican Republic to drum up support for his reinstatement.
Micheletti and Zelaya did not speak face to face as expected, but they each maintained that they should be the president of Honduras.
The Central American country of seven million inhabitants has been hit by protests since June 28, when Zelaya was seized by the army and forcibly deported.
Speaking on Friday in San Jose, the Costa Rican capital, Arias said: "I feel satisfied because a sincere, clear dialogue has been initiated, but still, the positions are very different and certainly these things ... take time, they require patience.
"This could possibly take more time than imagined."
Talks to continue
Micheletti, following his return to Tegucigalpa, the capital of Honduras, said he was ready to return to talks "if necessary", after earlier saying he was going back to Honduras "totally satisfied".
"If I am invited by President Arias, I will return with great pleasure," he said.
Micheletti and Zelaya have each left a team of negotiators behind in San Jose.
The US has suspended military ties with Tegucigalpa and is warning that it could sever $200m in aid.
The World Bank and the Inter-American Development Bank have frozen credit lines.
Zelaya's leftist allies in South America have also made life uncomfortable for Micheletti since the coup.
Venezuela has suspended its oil deliveries to Honduras, while Nicaragua denied Micheletti permission to fly through its airspace for the Costa Rica meeting.
The Honduran supreme court said, in advance of the San Jose talks, that if the congress granted Zelaya amnesty, he could return to Honduras without fearing an arrest warrant for treason issued against him.
Some Honduran politicians said they were open to an amnesty.
"It would be an acceptable formula to bring peace to the country," Anibal Solis, a Christian Democrat politician, said.
Zelaya attempted to return to Tegucigalpa 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.
Most Honduran business leaders have opposed any return of Zelaya.
"There has been an irreversible democratic transition in Honduras, and we're going to have to stick together to create jobs in the teeth of the global crisis and if there is international isolation," Adolfo Facusse, an employers' federation chief, said.
Zelaya was removed from power as he was about to press ahead with a non-binding referendum on constitution change.
Congress and the courts had declared the move to hold the public vote illegal, accusing Zelaya of trying to change the charter to enable him to run for a second term in office.
Any deal seeing Zelaya restored as president in Honduras would likely require him to drop those plans.
In Washington, the head of the Organisation of American States, Jose Miguel Insulza, said he believed there was "ample margin" for a compromise to be reached.
He stressed that the cornerstone of any agreement should be Honduras's de facto government allowing Zelaya to return.