A recent report by Dr Jim Elmslie, Co-ordinator at the West Papuan Project, said genocide, the forcible removal of children and other human right abuses are taking place in Indonesian-controlled West Papua.
“Since  many ten of thousands, if not hundreds of thousands of people have perished directly as a result of conditions that have been enforced upon them … this is why we characterise what is going on there as a genocide or a potential genocide,” Dr Elmslie told Fairfax Media's Breaking Politics.
On Monday, Mr Abbott made it clear that he would not allow activists to “grandstand” against Indonesia after the activists entered the consulate by scaling a wall and asked for Australia to aid 55 political prisoners jailed in Indonesia.
“Australia will not give people a platform to grandstand against Indonesia. We have a very strong relationship with Indonesia.
"People seeking to grandstand against Indonesia, please, don't look to do it in Australia, you are not welcome. The second point is the situation in West Papua is getting better, not worse,” he said.
Reports have also emerged that an Australian in the consulate forced the protesters to leave by threatening to call Indonesian police.
In rejecting Mr Abbott's claim, Dr Elmslie said that West Papuans ranked very poorly on measures of health and had the lowest socio-economic standing of the Indonesian population, with high rates of AIDS, and the lowest level of education.
“[Indonesian] soldiers have taken trophy videos of them torturing and killing West Papuan people … I was surprised to hear Prime Minister Abbott's comments.
“To me, the situation is not getting better it's getting worse.”
Dr Elmslie conceded that getting accurate information from West Papua is difficult.
Elaine Pearson, Australian Director of Human Rights Watch, said: “I don't think the situation is getting better; you'd only say that if you were blind and deaf to the situation.”
She said it is difficult to know the true story, but said it is clear the Indonesian government is trying “to stamp out any call for independence”.
“I don't think we have enough information to … characterise this as a genocide.
“Indonesia is a democracy … people should have the right to protest,” Ms Pearson said.
Comment has been sought from the Prime Minister's office. [SydneyMorningHerald]