A Melbourne man, allegedly part of the Anonymous online collective, has been charged over the revenge hacking of Australian intelligence agency websites.

Mathew John Hutchison faced Melbourne Magistrates Court this week, accused of urging Indonesian hackers to attack the websites of ASIO, the Australian Signals Directorate and Australia's overseas spy agency, ASIS.

The 21-year-old, from Melbourne's western suburbs, was alleged to have made contact with the Indonesian hackers, who were angered by revelations in October 2013 that the Australian embassy in Jakarta had allegedly been used for spying.

In retaliation for the alleged espionage activities, the Indonesian hackers, operating under of the banner of the Anonymous online collective, attacked a large number of websites belonging to private Australian businesses and organisations.

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The Australian Federal Police allege that Hutchison then published a video on a website, in which the Australian arm of Anonymous urged the Indonesian hackers to target the ASIO, ASIS and the Australian Signals Directorate websites instead of the other websites.

"You have defaced many innocent Australian websites in an effort to protest against the Australian Government and their spy agency, ASIO," the video said.

"Innocent businesses should not be attacked. We all bound together in an effort to bring down our tyrant governments to shape our world as a better place.

"We bid you, as a fellow brother to focus on your main target — governments and spy agencies and leave the innocent bystanders out of this.

"If you choose to disagree then you should feel the full wrath of our fellow legion."

Hutchison then allegedly published a second video, intended to serve as a "final warning", which warned the Indonesians that there would be "cyber war" if they continued attacking private websites.

Both the ASIO and ASIS websites were attacked and brought down for varying periods of time.

It is also alleged that Hutchison gave further instructions via another website to the Indonesian hackers.

He has been charged with two Commonwealth offences of "urging unknown person to commit an offence of causing an unauthorised impairment of electronic communication to or from a computer."

Hutchison has also been charged with possession of a laser pointer, and will face a committal mention on April 8, 2015.