Neil Gaughan relayed the conversation in an email to AFP staff on the evening of the June 4 raid, newly-released documents reveal.
“Good work by all involved,” Mr Gaughan wrote.
“I also received a call this evening from the Sec DHA (Secretary of the Department of Home Affairs) who is fully supportive of the actions of the AFP and ask (sic) me to pass on my thanks to the team involved.
“Well done — tomorrow is another day.”
The documents were obtained by the ABC under Freedom of Information.
The AFP raid on the Canberra home of News Corp (that owns news.com.au) reporter Annika Smethurst related to an article based on leaked government information.
With questions raised about his judgment, Home Affairs boss Michael Pezzullo has defended the telephone call.
“DC Gaughan is a colleague,” Mr Pezzullo told the ABC.
“In the discussion in question, I expressed my compliments to him and his officers on their professionalism and their diligent focus on independently enforcing the laws of the land, as the parliament has passed them.
“To conflate the expression of professional compliments to colleagues with a supposed attitude to press freedom is not an accurate comparison.”
Shadow attorney-general Mark Dreyfus wants to know more about the conversation in question.
“If that is so, that’s something I’ll certainly be very interested in hearing more details about,” Mr Dreyfus told reporters in Canberra on Thursday.
Asked about the investigation into Ms Smethurst and a separate probe into the ABC, which was raided by police the day after, Attorney-General Christian Porter told Sky News on Thursday they were ongoing.
Mr Porter reiterated his position that he would be “seriously disinclined to consent to a prosecution” of the journalists.
Meanwhile, a recent survey within Home Affairs found only 25 per cent felt they were valued for their contribution, 31 per cent believed senior executives communicated effectively and 35 per cent said their bosses were of high quality.
The department was rated last of 97 government agencies in terms of employee engagement and 94th for wellbeing.
Labor home affairs spokeswoman Kristina Keneally said it reflected a “poisonous culture” within the department.