[3][4] The AFP has a focus on preventing, investigating and disrupting transnational, serious, complex and organised crime including terrorism and violent extremism, cybercrime, child exploitation, drug smuggling, and human trafficking.

This followed a review of Australia's anti-terrorism capacity by Sir Robert Mark, former commissioner of the Metropolitan Police in the UK, which was commissioned by the Fraser government following the 1978 Hilton bombing.

[7] Separately, the National Anti-Corruption Commission (NACC) is charged with investigating systemic corruption in the AFP and other commonwealth agencies.

Key priorities of the AFP are set by the Attorney-General, through a "ministerial direction" issued under the Australian Federal Police Act 1979.

Uniform protection officers (identified as Protective Service Officers or PSOs) are firearms and defensive tactics trained, and perform duties which include armed escorts, bomb appraisals, bomb detection canines, visitor control, static guarding, alarm monitoring and response, mobile, foot and bicycle patrols, maintain civil order, security consultancy services, counter-terrorism first response at many Commonwealth establishments.

Protective Service Officers have powers under Section 14 of the AFP Act 1979 to stop, request identification, search and arrest within their jurisdiction.

Specialist Protective Command officers providing an armed uniform capability are located at federal establishments including Parliament House in Canberra; the residences of the prime minister and governor-general; foreign embassies and consulates in Canberra, Sydney, Melbourne and Perth; the Australian Nuclear Science and Technology Organisation, joint defence facilities such as the Australian Defence Force Headquarters in Canberra, Holsworthy Barracks, Garden Island Naval Base, Victoria Barracks, the Pine Gap US defence installation, and sensitive covert locations in Australia and internationally.

[11] On 6 December 2019 the AFP announced that the Protective Operations Response Team (PORT) members located at the nine designated Australian airports will carry the Daniel Defense Mk.18 Short Barreled Rifle.

In recent years, Australian government efforts to assist neighbouring and remote countries with institutional capacity building has led to AFP deployments to Papua New Guinea, the Solomon Islands (Under the Regional Assistance Mission to Solomon Islands), Timor-Leste (Under the Timor-Leste Police Development Program TLPDP), Nauru, Tonga, Vanuatu, Afghanistan, Samoa and Vanuatu.

The NDG brings together the AFP and its partner agencies to coordinate operational disruption activities nationally and internationally with the aim of countering the enduring threat posed by foreign fighters.

[23] In October 2006 a Cairns jury convicted pilot Frederic Arthur Martens under sex tourism laws of having intercourse with a 14-year-old girl in Port Moresby, Papua New Guinea.

[26] Over 200 heavily armed police conducted raids at 3:00 am at various houses in Victoria on 19 April 2015, and then held Harun Causevic on a Preventative Detention Order (PDO), before charging him with terrorist offences.

[28] However, after Causevic spent three months in jail awaiting trial the federal police decided to drop the terrorism charges.

[30] On 4 June 2019 the AFP conducted a raid on the home of News Corp journalist Annika Smethurst, looking for information connected to a story she had written a few years earlier about new laws that would give the security forces new powers for surveillance over Australian citizens.

[32] The next day the police raided the Australian Broadcasting Corporation (ABC) over a story about alleged war crimes in Afghanistan.

[34] The incidents caused an outcry of condemnation from international media outlets, including the British Broadcasting Corporation (BBC) and The New York Times.

[38][39] The inquiry was created in the wake of accusations of mishandling made by both the ACT's Director of Public Prosecutions, Shane Drumgold, and the Australian Federal Police against each other.

[46] The AFP was criticised for an operation in which it targeted a young boy with autism spectrum disorder who had developed a fixation on a terrorist organisation.

The boy's parent reported their concerns to authorities, leading to the Australian Security Intelligence Organisation, Victoria Police, and AFP joint counter-terrorism team (JCTT) to begin Operation Bourglinster.

Officers of the JCTT were accused of encouraging the boy's ideation with terrorism, leading to a Victorian court to impose a permanent stay on charges.