Mr Ramos-Horta, who will on Friday attend Timor-Leste's 20th-anniversary celebrations of its vote for independence, compared the Australian government's pursuit of the pair to the novel Les Miserables and Inspector Javert's obsessive pursuit of the convict Jean Valjean.
"I would never as leader of a country prosecute someone if we spied on some country and they came to us or the media and said I have just been asked to do something that is completely unethical and has nothing to do with the national interest," he said.
"I would apologise to the nation if I were leader, apologise to the gentleman, the spy."
Mr Ramos-Horta was shot at his home in Dili in an assassination attempt in 2008.
The scandal began in 2004 when the Australian Secret Intelligence Service planted covert listening devices in the Timor-Leste cabinet office to gain an upper hand in negotiations over the rich Greater Sunrise oil and gas fields.
Australian Prime Minister Scott Morrison and Timor-Leste PM Taur Matan Ruak will formally sign a maritime boundary treaty on Friday that splits revenue from the gas fields, with it to get 70-80 per cent.
Despite Australia being criticised in the International Court of Justice, Mr Ramos-Horta said Timor-Leste had come out of it with a better arrangement and he still regarded it as an aberration by a friend.
"The permanent maritime boundary is a better arrangement for Timor-Leste, we must get over it and Australia should get over it by letting go Witness K and Bernard Collaery," he said.
Protesters marched through Dili on Wednesday in support of the whistleblowers.
Mr Morrison will be the first Australian prime minister to visit the neighbouring country in nearly 12 years and will be joined by Foreign Affairs Minister Marise Payne and Opposition Leader Anthony Albanese.
Australia led and contributed the majority of troops to the INTERFET multinational peacekeeping force, which confronted widespread violence and intimidation carried out by pro-Indonesia militias led by Eurico Guterres around the 1999 referendum