In a report released late Friday, the group said it had information that could implicate "state agents" in four deaths and confirm that Roberto Micheletti's interim government had committed rights abuses.
At least two people had disappeared, including one "last seen at a demonstration on July 12" and another who "was taken from his home on July 26," said IACHR, an autonomous organ of the Organization of American States.
IACHR called for an "in-depth enquiry" into the four deaths, the first of which occurred on July 5 at the Tegucigalpa airport, where Zelaya made a first scuttled attempt to return home and be welcomed by throngs of supporters.
Isis Obed Murillo, 19, "was hit in the head with a bullet" during a standoff between Zelaya's supporters and security officials, who prevented the cowboy-hatted deposed president from returning to Honduras, the report said.
Two others were also shot in the head during demonstrations, and one man was found dead on July 25 near the border with Nicaragua, where Zelaya supporters had gathered and the leftist leader made a second, brief attempt to cross over into Honduras.
The man had been arrested a day earlier and "his body bore signs of torture," according to the report.
The group also criticized the "militarization" of impoverished Central American country in the wake of the coup, noting that the military was a constant presence at protests.
"Only reestablishing democratic institutions will guarantee the restoration of individual liberties in the country," the report said.
The mission is the second human rights delegation to criticize Micheletti's government for abuses in the wake of Zelaya's ouster.
In late July, a group of rights advocates including representatives from the International Federation for Human Rights, found that "serious and systematic" violations had been committed since the June coup.
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