The disclosure, by the Australian Broadcasting Corporation's (ABC) Foreign Correspondent programme, will raise questions about Mossad's frequently-used practice of recruiting dual citizens to work as undercover agents.
Mr Zygier, who was born in Australia but held Israeli nationality after emigrating to Israel, was discovered dead in his high-security cell in December 2010 some 10 months after being incarcerated in Ayalon Prison in Ramla, near Tel Aviv.
Israeli officials say he committed suicide but kept his death a secret until last week when ABC reported that he was an Australian citizen and worked for Mossad.