De facto leaders say deposed president can appeal to congress for reinstatement.
Police said he had bullet wounds to his head and chest, and that his hands were tied behind his back.
The body of another, unidentified man was found nearby.
Members of the Honduran congress voted Roberto Micheletti to the interim presidency after soldiers forced Manuel Zelaya from the presidential palace on June 28.
There have been several rounds of negotiations between delegates for Micheletti and Zelaya in recent weeks but the rival sides have failed to reach a deal to end the political crisis.
In an apparently unrelated attack, army Colonel Concepcion Jimenez was shot dead on Sunday night outside his home in Tegucigalpa, the Honduran capital, the military said.
Ramiro Archaga, a military spokesman, said that no motive had yet been established for the killing.
Jimenez managed the Military Industry of Honduras, an agency that makes uniforms for Honduran troops.
Honduras has the highest murder rate in Central America, much of it related to illegal drugs. About 7,235 people in the country of 7.7 million were killed in 2008 – a 25 per cent increase from 2007.