Australia was told through ''intelligence channels'' that Australian Ben Zygier had been imprisoned in 2010 by Israeli authorities on ''serious offences'' under Israeli national security law, Foreign Minister Bob Carr has confirmed.

Mr Carr's comments come as Israel admitted for the first time that it held an Australian with dual citizenship under a false name for security reasons.

According to a statement on Wednesday from the Israel's Justice Ministry, Ben Zygier's Melbourne family was notified after he was detained. Zygier was reportedly known as ''prisoner X'' in the high-security jail.

Facing a Senate estimates committee on Thursday morning, Senator Carr said the Australian government was given assurances by Israel that Mr Zygier's rights would be respected.