The United States on Friday praised Indonesia as upfront in its investigation of torture of Papuan detainees and said it would not affect a resumption of military ties.
Human rights activists have criticized the US decision this year to restart military training to the elite military unit Kopassus, pointing to what they call a culture of impunity for abuses.
But State Department spokesman Philip Crowley said that the Indonesian government had promised a "full and transparent investigation" after an online video surfaced of the beating and humiliation of detainees.
"They have undertaken, under democratic law, specific reforms and we will continue to work with them," Crowley told reporters.
"What they announced today is consistent with terms under which we resumed limited security cooperation with Kopassas," he said.
The United States has been seeking to expand relations with Indonesia, seeing the moderate Muslim-majority nation as an ideal ally. President Barack Obama is due next month to visit Indonesia, where he spent part of his childhood.
Defense Secretary Robert Gates visited Indonesia in July and announced a resumption of ties with Kopassus after a 12-year hiatus but said the engagement would be limited until the army undertakes reforms.
In the video, soldiers are seen applying a burning stick to the genitals of an unarmed man and threatening another with a knife as they interrogated them over the location of a weapons cache.
Foreign media have minimal access to Papua, whose people are racially distinct from the majority of Indonesians and have long spoken of ill treatment.