Varghese said he did not know if the then-Foreign Minister Stephen Smith had been briefed.
"It's entirely possible that the minister might well have been briefed orally and given the nature of this case, that wouldn't surprise me," Varghese said.
"But since I don't have proof one way or another, I'm simply saying that I'm investigating that further," he added.
Varghese conceded that it was unusual for Australia to use security channels to seek assurances from a foreign government about the rights of a citizen.
"No, it's not normal practice and this is not a normal case," Varghese said.
"The initial advice that came to us on this case was through intelligence channels and the communication on this case has essentially remained through intelligence channels," he added.
He declined to say whether Australia's main spy agency ASIO or the highly secretive spy agency operated out of Australia's overseas diplomatic missions, ASIS, was the Australian intelligence channel that provided the information.
He also declined to comment on media reports that Zygier had been under investigation by ASIO.
Carr had told Australian Broadcasting Corp. television in a program that aired on Tuesday that his department only became aware of Zygier's arrest after his death when his family asked for his remains to be repatriated.
Carr corrected the record on Wednesday and ordered his department to review its handling of the case.