Filep Karma, the most prominent pro-independence Papuan to have been incarcerated in Indonesia, was held up for questioning by military and police officers at Jakarta's main airport.
It is two years since Filep Karma was released from prison after serving 11 years for treason for raising the banned Papuan nationalist flag, the Morning Star.
Flying in to Sukarno Hatta airport from Yogyakarta, Mr Karma caught the attention of a military, or TNI, officer due to the customary Morning Star badge he wears on his shirt.
He was taken in for questioning by the airport police squad, and interrogated about his activities.
While the national constitution allows citizens to express cultural identity, Indonesian authorities take a dim view of Papuans expressing aspirations for independence.
Mr Karma denied he was breaking the law by wearing a small symbol on his shirt.
He said the security officers tried to link him to armed elements of the Free West Papua movement, or OPM, but his credentials as a peaceful advocate for independence are well established.
At the time of Mr Karma's release from Papua's Abepura prison Indonesia's Political, Law and Security Minister, Luhut Pandjaitan, said the Papuan had been wrongly convicted of treason, or makar, which implies inciting armed revolt.
He had served 11 years of the 15-year sentence.
This week, security forces took Mr Karma in again briefly.
Released after almost three hours of questioning, Mr Karma revealed that officers had become aggressive to him, calling him a monkey.