East Timor alleges Australia spied on the Timorese during oil and gas negotiations in order to extract a commercial benefit.
East Timor says the spies' lives could now be at risk.
"We looked through documents quite thoroughly back in those days and we were able to pick up some names, people we believe were part of the teams coming in at different times," Timor's Petroleum Minister Alfredo Pires told SBS.
"We've identified also a lady spy that was probably part of the team.
"We know espionage is a dangerous game, we do have those names we've deducted ourselves, we've written in our computers.
"Nowadays people can get access to your computers, get information, come into my computers, get the files, if those people are in any way still active in this world carrying out similar work - they happen to be working in some of the AusAid program - they better take appropriate measures because it could be dangerous for them. Their life could be at risk."
Relations between the neighbouring nations has been rocked by last week's raid on the home of the first whistleblower - reportedly a former senior spy who oversaw the bugging of the Timorese cabinet room in 2004.
The impoverished country has taken the matter to the Permanent Court of Arbitration in The Hague, after initially raising spying concerns with the Australian government about a year ago, but got an unsatisfactory response.
The office of former ACT attorney-general Bernard Collaery, a lawyer acting for East Timor in The Hague, was also raided - actions that East Timor's Prime Minister Xanana Gusmao denounced as "unconscionable and unacceptable conduct".
Minister Pires says he believes some of the Australians involved in the alleged spying were working for AusAID.
"The aid program was used for faciliating what was carried out back in Timor. That is something we find very disappointing. Timor Leste has been assisted by Australia quite a bit, particularly AusAID programs, a lot of genuine people doing a lot of good work back in Timor, now we've learned this we become suspicious. Who do we trust in the aid program?"
Watch the extended interview with Minister Pires on YouTube:
