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| Aksi Damai Rakyat Papua |
Mr Kogoya was arrested along with dozens of other activists in a raid on their headquarters in Jayapura on Sunday night.
Authorities said they had been searching for him for over a year, and claimed he was responsible for a number of recent attacks on civilians.
They said the arrest would deal a major blow to the OPM, which John Otto Ondawame, the organisation's international spokesman, has denied.
"It doesn't mean anything. Even if they kill a thousand West Papuans, members of OPM or civilians, we will continue and grow. The deep aspiration of independence for West Papua will never die," he told Radio Australia.
The raid was carried out by a number of police groups, including members of the Australian-trained elite anti-terrorism unit, Detachment 88.
Jakarta's crackdown
Jason Macleod, from the University of Queensland's centre for peace and conflict studies, said it was the second raid of its kind in as many weeks, and shows Indonesian authorities are cracking down on the movement.
"Without a doubt we are seeing an increase in police and military operations," he said.
"Activists have been arrested in other parts of West Papua. We're also seeing an increase in surveillance activities, so a number of the West Papua national committee activists have gone to ground, many are in hiding and a number of church leaders and civil society leaders are also reporting that West Papua is more unsafe than they've experienced it in many years."
However, Jason Macleod agreed it was unlikely that Daniel Kagoya's arrest would reduce the strength of the OPM.
"The most important thing to remember is that the overwhelming majority of the population want independence, and that would be true for political leaders, church leaders, NGO activists, right through to grassroots," he said.
