The meeting with Clinton marks Zelaya's highest-level talks with US officials since being overthrown and forced into exile on June 28, and could be a signal that Washington may be willing to provide more than just vocal support for him.
Roberto Micheletti, Honduras' interim president, announced on Tuesday that the country's caretaker government has accepted Oscar Arias, Costa's Rica's president, as a mediator in the crisis.
"We've accepted him as the mediator, given the high profile that the president of Costa Rica has," Micheletti told local radio in Tegucigalpa.
Zelaya could come back to Honduras if Congress granted him amnesty, a spokesman for the Supreme Court told the AFP news agency on Sunday.
Zelaya attempted to return to Tegucigalpa, the Honduran capital, on Sunday but soldiers and military vehicles blocked the runway and warned off Zelaya's aircraft.
At least one person among the thousands waiting for the aeroplane to land was killed by security forces - the first to die in clashes since the coup.
Several thousand pro-Zelaya demonstrators took to the streets on Monday, marching to the presidential palace and shouting "murderers" at soldiers.
But with a night-time curfew still in place, the protest ended peacefully and demonstrators headed home.
'Acts of violence'
The US has condemned the violence against protesters and reiterated calls for Zelaya's reinstatement.
"We deplore the use of force against demonstrators in Tegucigalpa in recent days and once again call upon the de facto regime and all actors in Honduras to refrain from all acts of violence," said Ian Kelly, a spokesman for the US state department.
|Mourners preparing to bury Oved Murillo, 16, who was killed in Sunday's violence [EPA]
In a phone interview with Al Jazeera, Martha Lorena Alvarado, a Honduran minister, defended Sunday's security operation.
"We are trying to put this country in order because Mr Zelaya wanted to have a replica of Venezuela. If you have ever been to Venezuela, you can foresee our future for the next 20 years," she said.
"People have the right to demonstrate but they do not have the right to disrupt with rocks, destroying everything and defying the police."
Zelaya was removed from power as he was about to press ahead with a non-binding referendum that his domestic critics said was aimed at changing the constitution to enable him to run again for office.