Indonesian militant Abu Dujana plans to sue the police, alleging he was shot in the thigh by members of an elite anti-terrorist unit after surrendering, one of his lawyers says.

Dujana, who is believed to head a military wing of the South-East Asian militant group Jemaah Islamiah (JI), was captured on June 9 during a police raid in Central Java.

Lawyer Achmad Michdan said the country's anti-terrorism unit, Detachment 88, had violated the suspect's rights by shooting him after he had surrendered. "We will sue the Indonesian police and Detachment 88 and we will ask the court to examine the basis and the process of the arrest," he told Reuters.

National police spokesman Sisno Adiwinoto said the arrest had not violated human rights. "We have long upheld the principles of human rights in our operations and we have acted according to the procedures," Adiwinoto said.

Dujana had been sought in connection with several attacks, including the 2004 Australian embassy blast and the Marriott blast. Police said he also had a role in the 2002 Bali bombings, which killed more than 200 people, including 88 Australians, many of them foreign tourists.

Dujana said in a video shown at a police news conference last week that he had undergone military training in the Pakistani city of Peshawar and in Afghanistan. He also admitted in the video to being head of JI's armed wing.

Lawyer Michdan cited eyewitness reports that the police shot Dujana in the leg in front of three of his children while he was squatting with his hands raised after being forced off his motorbike.

"Any law enforcement activity should abide by the principles of human rights. A person who has surrendered should not be shot at and definitely not in front of his children and neighbours, who knew him as a good person," he said.

Michdan said the lawsuit would be filed after Dujana's wife and four children were allowed to see the suspect. The family has not been allowed to visit him since he was detained.