Home Affairs boss Mike Pezzullo personally rang to Australian Federal Police Deputy Commissioner Neil Gaughan to congratulate him on the raid of the home of a Canberra journalist, an operation in planning for more than three months, according to a tranche of internal police documents.
Separate documents also reveal the cost of the Australian Federal Police investigations into the high-profile Afghan files and Australian Signals Directorate leaks have reached nearly $300,000.
The Pezzullo call, detailed in emails obtained by Senator Rex Patrick under freedom of information, came hours after police had finished executing a search warrant on the Kingston home of Newscorp journalist Annika Smethurst in June.
Smethurst's story, published in April 2018, alleged the heads of Defence and Home Affairs discussed new powers to allow the Australian Signals Directorate to spy on Australians for the first time, based on leaked classified documents. The intelligence agency is currently restricted to gathering intelligence and fighting cyber crime offshore.
Through email, Deputy Commissioner Gaughan said he'd received a call that evening from the "Sec DHA", who was "fully supportive of the actions of the AFP and pass on my thanks to the team involved".
"Well done - tomorrow is another day," the deputy commissioner said, finishing with a smiley-face.
A separate email from an unknown party was also glowing of the way police handled the raids.
"You and the team are presenting the AFP in its finest light. Let's hope the next few days continue as today did, professional, considered but assertive in order to achieve the investigative outcomes we were all expected to achieve in the office we hold," the mystery sender said.
The documents also include briefings dating back to February, indicating the raid had been months in the planning.
A handwritten note scrawled on one of the briefings said the execution of the search warrant was "necessary" to seize material "which will inform elements of the offences".
Text messages have also been released that reveal AFP Commissioner Andrew Colvin was in touch with officers on the ground as soon as they entered Smethurst's home.
"FYI only - in case your phone starts ringing...we've just entered the door of the journo. Everyone that needs to know knows," one message said.
"Good man," Commissioner Colvin replied.
Separately the AFP has confirmed the cost of the investigation into the leak ran to $134,900, as of August 6, excluding legal costs.
A newly published letter also shows Defence secretary Greg Moriarty made a formal request to police to investigate the leak two days after the story was published.
Mr Moriarty described the material in the story as "highly classified" but did not specify any national security harm caused.
The supporting material checklist, usually required for a police referral, was also not filled out because of the secretive information involved.
It is unclear why it took more than a year for the investigation to reach the point where a search warrant was justified.
But it also took nearly two years for the AFP to carry out a search warrant on the ABC's headquarters in Ultimo related to a different leak, the day after the Canberra raid.
The ABC first published allegations of war crimes carried out by Australia's special forces in Afghanistan, based on hundreds of pages of classified documents in July 2017.
Former military lawyer David McBride is currently facing charges in the ACT Supreme Court over the leaks.
Police figures show the cost of investigation into the Afghan files leak has reached $140,600. This doesn't include legal costs.
An email to Deputy Commissioner Gaughan after that raid said it went as well as could be expected "apart from the constant tweeting and filming".
Police have not ruled out charging Smethurst or ABC reporter Dan Oakes over the publication of the material.
Mr Pezzullo told the press freedom inquiry the person who leaked the Australian Signals Directorate material should also be jailed. Police are believed to be closing in on the suspect.