Arrested in the afternoon of 17 September 2019 in Abepura, Papua, by Papua Regional Police without arrest warrant. He is the chair of KNPB and accused of the intellectual actor behind the uprising. Besides Articles 106 and 110, he is also indicted with Articles 160 of the Criminal Code and Article 82 section (2) of Law Number 2 Year 2017 regarding Societal Organisations. He told his lawyer that he participated on the 19th of August protest, but only monitored the 29th August protest from his organisation’s secretariat. When arrested, he was on a motorbike with his friend Donny Itlay. The latter was arrested as well, but charged over theft of his rented motorbike. Itlay’s verdict of 7 months imprisonment was delivered on 18 February 2020.

On 4 October 2019, Agus Kossay and six other prisoners were transferred from Papua Regional Police Detention Center, Jayapura, Papua Province to East Kalimantan Province for “security reasons”. This transfer was in breach of Indonesian criminal procedure law; it was conducted, inter alia, without informing their lawyers and families, and without the requisite approval from the Supreme Court. Further to these breaches, the transfer has resulted in a significant increase in legal aid costs (due to the airfares needed to attend each trial), and has cut the prisoners off from their families and culture.

He was detained in Balikpapan Prison Class IIB, Balikpapan, East Kalimantan Province until his release on 12th August 2020.