Australia-based anthropologist Yamin Kogoya said there is too much emphasise on ramming the Indonesian state ideology down Papuans' throats.
Indonesia's president Joko Widodo has pushed major infrastructure development projects in Papua in the past three years.
But Mr Kogoya said the government's approach sees Papuans as a threat or even second class citizens in need of handouts. He urged Jakarta to develop Papuan human resources.
"See Papuan people as a human being who have history and language. These people have survived in this part of the world for millenia. And I think Indonesia, after 60 years, they don't really fully understand the value system and the culture and the language of the Papuan society."
Mr Kogoya said another major factor inhibiting Papua's development was the presence of Indonesia's military. He said the effect of having a military or police post in every town and many villages in Papua could not be under-estimated.
"These people, they're fully armed and carrying around these big machines guns and weapons. You don't use this sort of mechanism to help people understand the value system of Indonesia as a nation," he said.
According to him, the military's involvement in education in Papuan villages was problematic. "You see Indonesian military going to the villages and starting teaching the Papuan children in their village schools," he explained.
"I have experienced this many times when I was growing up in the village, in the Highlands. They obviously don't use the curriculum or have clear guidelines, but they go in there with their weapons where the children can see."
According to Mr Kogoya, this was how the military sought to teach Papuan children about the state ideology regarding the integrity of the Indonesian republic, and the Pancasila ideology. "If you want Papuan children to love Indonesia, this is not the way to do it," he said.