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The Australian government has rejected reports it is investigating allegations that Indonesia’s elite counterterrorism unit tortured suspected separatists in Maluku.

An Australian foreign ministry official previously said Canberra was concerned about the allegations by Amnesty International and Human Rights Watch, and that officials from its embassy in Jakarta had visited Ambon in Maluku to check them out.

Australia channels millions of dollars each year to Densus 88, the Indonesian National Police’s counterterrorism unit.

On Tuesday, however, an embassy official denied there was an investigation going on.

“An embassy officer visited Maluku recently as part of a regular program of provincial visits,” a spokesman said.

“In that context, publicly available reports of allegations against the [Densus 88] Maluku Unit were raised with local government officials and NGOs. Any investigation is a matter for Indonesian authorities.”

Densus 88 is said to have tortured 12 of 21 suspected separatists arrested last month for allegedly possessing an outlawed South Maluku Republic (RMS) flag.

Police accused the suspects of trying to hoist the flag during President Susilo Bambang Yudhoyono’s visit to the province on Aug. 3 and disseminate posters, books and other material concerning alleged human rights violations in Maluku to foreign dignitaries and journalists.

National Police spokesman Insp. Gen. Marwoto Soeto said police had launched an investigation into the torture claims.

“If they’re true, the officers could face charges,” he said.

Sophie Richardson, the interim Asia director for New York-based HRW, urged Australia to get involved in the investigation.

“The Indonesian government has made multiple rhetorical commitments to greater police accountability... which have proved to be empty pledges,” she told the Globe. “The Australian government must investigate these torture allegations.”

However, Hikmahanto Juwana, an international relations expert from the University of Indonesia, said the Indonesian public might regard Australian involvement in a probe as interference.

“Australia must use only existing diplomatic channels to ensure these allegations are investigated,” he said.

“Since the claims were made, Australia has been trying to appease its own people, who are calling for more accountability over the funding for Densus 88.”

Semuel Wailaruny, from the Maluku People’s Advocacy Team, has said Densus 88 tortured many people at its provincial office.

“They were blindfolded with duct tape and scarves so they wouldn’t see their attackers,” he told the Globe on Monday.

“They were beaten. Their heads were slammed [against] walls and they were kicked in the stomach. One of them, Yonias Siahaya, was left a cripple. He is paralyzed from the waist down.”

However, Maluku Police spokesman Adj. Sr. Comr. Johanis Buai denied the accusations.

The allegations came as another Maluku prisoner, Yusuf Sipakoly, died on Monday from injuries his family says were sustained during torture, and for which he was denied treatment.