It called for the establishment of an international war crimes tribunal akin to those for former Yugoslavia and Rwanda to try officers responsible for the bloodshed.
Wiranto has denied all charges and said they were part of a smear campaign to sidetrack his candidacy.
According to unconfirmed reports, the US State Department has placed Wiranto on its visa watch list, which would bar his travel to the US.
Still, Deputy Defense Secretary Paul Wolfowitz and other Bush administration officials have pressed for lifting the congressional ban on military ties with Indonesia, broken off by the Clinton administration because of the bloody rampage by Wiranto's troops in East Timor.
Wolfowitz, a former ambassador to Jakarta, developed close ties with Indonesia's hardline generals and sees the armed forces as important allies against Muslim radicalism in Southeast Asia.
"If he does travel outside Indonesia, Wiranto should be arrested and transferred to East Timor," the human rights group said.
The July elections will be the first direct election for president. Previously, lawmakers chose the head of state.
"This is a serious setback to the cause of human rights in Indonesia," said Munir, who heads Jakarta's Imparsial human rights group. "I fear democracy will suffer as a result."
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