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Bernard Collaery, a former Attorney General for the ACT and currently in The Hague in the Netherlands where he is preparing an espionage case against Australia, said papers were seized from his office.
He told ABC Radio: "I have no way at this moment of knowing the legal basis upon which these unprecedented actions [took place] - raiding my law offices to procure evidence which is about to go on the table in The Hague."
Federal Attorney General George Brandis confirmed that ASIO executed search warrants at addresses in Canberra.
"Documents and electronic media were taken into possession," Senator Brandis said in a written statement.
"The warrants were issued by me on the grounds that the documents contained intelligence related to security matters."
He rejected reports that the warrants were issued in order to affect or impede the current arbitration between Australia and Timor-Leste at The Hague.
"Those allegations are wrong," Brandis said.
"I have instructed ASIO that the material taken into possession is not under any circumstances to be communicated to those conducting those proceedings on behalf of Australia."
Australia's external spy agency, ASIS, is alleged to have covertly recorded Timorese government ministers and officials in Dili in 2004 during oil and gas negotiations.
There is also a report that a whistleblower, a former security officer who provided information to Collaery, has been picked up in a separate raid in Canberra.
Frank Brennan, a Professor of law at the Australian Catholic University, said: "A retired ASIS agent, he and his wife were detained and he was questioned for some time. Whether or not he was arrested - I am not apprised of that information. But I can tell you that on Thursday these proceedings were to begin at the Hague with the arbitration, and the understanding was that the parties were to determine how to deal with the witnesses, particularly this key whistleblower."
Paper and electronic documents taken by two ASIO officers from the Collaery's office relate to claims Australia inserted listening devices into the wall of the East Timor government's cabinet room.
Collaery says the listening devices were planted under the guise of refurbishing provided by an Australian aid project.
On ABC's PM program, Collaery said:
"The evidence is here. I can't see what the government hopes to achieve by this aggressive action. It can attempt to nullify the whistleblower's evidence, but that evidence has flown - the evidence is here, it's abroad, it's ready."
East Timor has likened the bugging to insider trading, a crime, in which one party to a negotiation knows what the other is thinking.
Collaery has worked with the Timorese for 30 years, according to his website.