East Timor wants the Treaty on Certain Maritime Arrangements in the Timor Sea (CMATS), declared invalid and the retired ASIS agent has sworn an affidavit detailing the alleged spying operation, which he led. Premises of the ex-agent and the lawyer representing the East Timorese government in arbitration over CMATS, Bernard Collaery, were raided by ASIO last week.
Mr Pires said East Timor wanted the seized documents returned, at least those that do not relate directly to security matters.
He said the alleged espionage by spies undercover as aid workers had ruptured trust.
"The allegation that aid was used as a cover for espionage is very disturbing," Mr Pires said.
"I know many aid workers from Australia. They are good people and this doesn't help them."
It was a sentiment endorsed by Stephen Howes, director of the Development Policy Centre at the Australian National University.
"It's obviously not good for aid agencies, for the relationship of trust required for an aid program."
He pointed to the CIA using a fake polio vaccination drive as part of its attempt to track down terrorist leader Osama bin Laden.
After it was disclosed, at least nine Pakistani health workers involved in polio eradication were killed and the United Nations withdrew its program.
Clinton Fernandes, a former army intelligence officer now with the University of NSW, said an inquiry was necessary.
"The use of the aid program to facilitate espionage, if true, is so serious that the person who is responsible for it ought to resign," he said.
The former ASIS officer has alleged former foreign affairs minister Alexander Downer ordered the operation, Mr Collaery said.
Mr Downer has declined to comment on intelligence matters, citing long-standing practice.