The Department of Foreign Affairs and Trade was blindsided by the Prime Minister Scott Morrison's admission he did try to invite Hillsong pastor Brian Houston to the White House.
However its top official has claimed the national interest and personal interests of the Prime Minister are "closely linked", during a Senate estimates hearing on Thursday.
Mr Morrison has gone to extraordinary lengths to avoid answering questions about the matter, since it was reported his request to include Mr Houston on the guest list for the Washington state dinner was vetoed by the US administration in September.
He danced around it in interviews and invoked public interest immunity over documents. Freedom of information requests on the topic were also refused.
Departmental officials suggested last year a confirmation could harm international relations.
But after Mr Morrison's surprise admission on Tuesday, DFAT secretary Frances Adamson said her officials had no "visibility" of the Prime Minister's request as it was managed by his office.
Officials later clarified DFAT officials in Washington probably would have known as they were coordinating the trip. However they did not tell DFAT in Australia and were acting as Prime Minister and Cabinet officials.
Labor senator Penny Wong accused the Prime Minister of orchestrating a cross-agency cover-up.
"He didn't want to answer the question so then the whole public service had to fall in line with that position," Senator Wong said.
DFAT's chief legal officer James Larson said hypothetically, disclosing such a matter could have hurt international relations, as it would have revealed the decision-making processes of the other nation.
Labor senator Tim Ayres asked whether the Prime Minister's disclosure this week have compromised the United States' confidence in Australia as a reliable recipient of information.
"That was very much a matter for the Prime Minister and I'm sure his US hosts would have understood the context in which it was made," Ms Adamson said.
Senator Ayres asked, "So it was vital not to disclose right up until the moment the Prime Minister did it on live radio himself?"
"That's correct," Ms Adamson replied. "Then the situation changes."
"That's not a matter of the national interest. That's a matter of the Prime Minister's interest isn't it?" Senator Ayres said.
"The two are often closely linked," Ms Adamson replied.
"The Prime Minister's personal and political embarrassment is linked to the national interest?" Senator Wong asked incredulously.
"No the decision by the Prime Minister to say what he said is absolutely his to make up until that point," Ms Adamson said.
Senator Wong contended the decision was not made in the national interest, but for the Prime Minister's "personal and political" benefit.
"There was a national interest issue used to try and cover up the fact the request was made and to prevent officers from disclosing it," Senator Wong said.
"Somehow there's no national interest impinged upon when the Prime Minister chooses to disclose it."
"I'm sure President Trump lies awake at night concerned about this issue," Liberal senator Eric Abetz interjected dryly.
Senator Wong: "He spent months avoiding this question. He's had departments prepare statements, he's had public interest immunity claims, he's avoided the question in the house ... all because supposedly this was going to harm the US relationship. And then he decides it's politically better if he gets it out and he goes on radio to disclose and all of a sudden that doesn't harm the US relationship."
Mr Morrison has attracted criticism over his friendship with Mr Houston.
The royal commission into institutional child sexual abuse found the high-profile Hillsong pastor failed to alert police to allegations that his father, Frank, had sexually assaulted children.