Commissioner Virginia Bell announced Mr Richardson's sudden departure on Wednesday night, as her inquiry prepares for its initial report by the end of April.
Prime Minister Anthony Albanese announced the royal commission following the Bondi Beach terrorist attack, in which 15 people were killed on December 14 when a father and son opened fire on a Hanukkah celebration.
"As I noted at the commission's initial hearing, Mr Richardson was uniquely well placed to advise on the material to be sought from our intelligence and security agencies in order to assess the effectiveness of their preparedness for, and response to, a terrorist attack," Ms Bell said in a statement.
"Thanks to Mr Richardson and the senior members of his team, Tony Sheehan, the former Commonwealth counter-terrorism co-ordinator and deputy director-general of ASIO, and Peter Baxter, a former deputy secretary at the Department of Defence and director-general of AusAID, work on the interim report is well advanced."
Ms Bell thanked Mr Richardson "for the valuable contribution he has made to the commission".
Her statement did not provide reasons for Mr Richardson's resignation.
Mr Albanese's government initially refused to call a royal commission into the Bondi massacre, instead tapping Mr Richardson to head a review of the adequacy of intelligence and law enforcement agencies before the attack.
Following weeks of political pressure, Mr Albanese relented and announced broader inquiry to be headed by Ms Bell, a former High Court judge, to investigate anti-Semitism and any failures in the nation's intelligence services.
Mr Richardson's review was folded into the new royal commission.
The inquiry is due to deliver its interim report to the government by April 30.
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