Investigation by Amnesty, Haaretz, Tempo and others finds links between official bodies and agencies from at least 2017.
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Comments met with surprise since US president has sought to deepen ties with key ally Japan, as well as India.
Government pledges action after tens of thousands of people rally over killings of women by their partners.
Sumatran orangutan named Rakus was seen using a plant to treat a facial wound possibly sustained during a fight.