The attack is part of a rise in violence directed against pro-independence Papuan activists in the Indonesian province. Analysts believe the attacks are a response to activists holding sensitive talks about forming a unified front to negotiate rights with Indonesia.
Mr Waromi, who heads the West Papua National Authority, has reportedly been receiving death threats. His daughter was found semi-conscious near a stream after the 18-hour ordeal.
"They beat her, tortured her, and now she can't speak because she's been traumatised," said Reverend Socratez Sofyan Yoman, the chairman of Papua's Baptist Church.
Reverend Yoman said the human rights situation in Papua had deteriorated, despite a 2001 "special autonomy" agreement negotiated with Jakarta. The agreement was meant to devolve local governance to Papuans, but Reverend Yoman said the Indonesian military had increased troop numbers in the province and human rights abuses continued. He said Indonesian migration to the province had also increased.
"It's a terrible situation in West Papua the special autonomy agreement has failed," Reverend Yoman said. "We want to make a genuine peaceful dialogue (with Indonesia) mediated by the international community to solve the West Papuan problem."
Dino Kusnadi, a spokesman for the Indonesian Embassy in Canberra, denied that the attacks on activists were committed by the Indonesian military or police. "The attacks on activists (are) criminal rather than political," he said.
Mr Kusnadi said he travelled to Jayapura last month with Indonesian ambassador Hamzah Thayeb and a delegation of 35 Indonesian officials to observe the status of the special autonomy agreement.
He said it was working and that reports by human rights groups were "very far from the truth".
Mr Kusnadi said troop increases in Papua were due to the establishment of a naval base there.
But Damien Kingsbury, an Indonesian expert at Deakin University, said the troop increase started before the naval base's establishment, and the military was predatory.
"Because troops are not adequately funded by the Government, they have to make a living from local activities, and that's usually around things like extortion and protection rackets," he said.
"There's been a rise in attacks against West Papuan leaders and organisations because the army is concerned about the possibility that West Papuans are getting organised to take a claim to the international community."