The Australian government has confirmed that it is investigating reports that an Australian-owned mining company was involved in ongoing Indonesian military operations in Paniai, West Papua.

In a statement received by the Jakarta Globe on Thursday, Australia's Department of Foreign Affairs and Trade confirmed it was aware of the reports but said there was no Australian government connection to the operations, which have been condemned as brutal by international nongovernmental organizations.

A ministry spokesperson said any inquiries regarding the involvement of the company – identified as Paniai Gold, a fully owned subsidiary of Melbourne based gold mining company West Wits Mining – should be directed to the company itself. "We are seeking to speak to the company about the reports," the spokesperson said.

Australia-based activist group West Papua Media, in a statement, alleged the Australian-trained joint police and military counterterrorism unit Detachment 88 (Densus 88) was involved in the allegedly bloody military operations.

The nongovernmental organization said that according to reports from Marisan, the director of the Papua branch of the Institute for Human Rights Study and Advocacy (Elsham), Densus 88 had been embedded with police Mobile Brigade (Brimob) units during operations against suspected members of the West Papua Liberation Army (TPN), based at Eduda, Paniai.

Marisan was quoted by WPM as saying that a total of 30 had died in the latest violence, including 17 people shot dead during the military operations in Eduda.

"Only ten of these victims were members of the TPN," the director was quoted as saying, adding that prior to the military operations, Brimob had also shot dead eight Papuans.

WPM said that Marisan and Yones Douw, a human rights defender based in Paniai, had both alleged that helicopters used by Paniai Gold on its Derewo River Gold project "were utilized by the military and police in these latest military operations."

A local source, requesting anonymity, told West Papua Media that the helicopters were those used by the mining company. "They are white with blue and red markings" the sources said. "They are defiantly mining company helicopters."

WPM said it had not been able to contact Paniai Gold's operations manger Vincent Savage, a non-executive director of West Wits, for comment.

The NGO said the 2011 November-December military operation was not the first in the area. "Paniai was the scene of widespread military operations between 1963-1969, 1977-1978, and again in 1981-1982. During this period US supplied Bronco aircraft that were used to bomb villages while helicopters strafed Papuans with machine gun fire."

The Australian foreign ministry reiterated that Australia had long recognized of the territorial integrity of Indonesia, "including by signing and ratifying the Lombok Treaty between both countries."

"Australia does not support independence for the Papuan provinces. The best chance for a secure and prosperous future for the people of Papua and West Papua lies within an integrated Indonesian state."