As political pressure mounted, however, Turnbull's news conference on Thursday changed the tone entirely - threatening a split between his Liberal Party and Joyce's National Party that potentially has far-reaching implications.
Barnaby Joyce: in regards to comments by the PM - in many instances they caused further harm.
Many members of the National Party believe the PM's comments were aimed at making Joyce resign.
"I would not wish on friend nor foe, the hurt, the scrutiny, the intense intrusion into your lives that I have gone through, through this process", Mr Joyce said.
For every Starts at 60 reader who has said that Joyce's behaviour deserves thorough examination because it says so much about his personal judgment as a public representative, not to mention the allegation of misuse of public funds, there is another one who doesn't give a damn about politicians' behaviour and just wants them to get on with governing.
The pair moved in together after Joyce separated from his wife past year.
Barnaby Joyce has hit back against Malcolm Turnbull in a powerful press conference held earlier today.
The Prime Minister also announced on Thursday that Finance Minister Mathias Cormann will be the Acting Prime Minister during his visit to the U.S. and urged Joyce to take a few days off to reflect on the situation.
Rahul releases 'guide to looting India' over Nirav Modi fraud
He further added that: "LoUs had not been converted into funded transaction so far, so it is a contingent liability". The ED has enllarged its probe to look into the charge of fraud of Rs 11,400 crore, agency officials said.
Barnaby Joyce has suddenly taken a week's leave.
While the rule will be hard to enforce, it will give Mr Turnbull a mechanism to sack ministers who engage in behaviour like Mr Joyce's in the future.
"I listened to it and thought that it was completely unnecessary - all that is going to do is basically pull the scab off for everyone to have a look at".
The existing ministerial code of conduct is "truly deficient", Turnbull said as he pledged to overhaul it in an effort to prevent such breaches in the future.
Turnbull's government formed by center-right liberal and conservative parties, including the National Party of Australia led by Joyce, has been under fire over various issues for a long period of time.
Mr Joyce contradicted the account of the businessman, Greg Maguire, about how he came to be given the rent-free apartment, valued at about $14,000, as Labor raised concerns over the businessman's dealings with the Agriculture Department.
The comments were seen as a thinly veiled call for the National Party leader to resign from cabinet, but Joyce, a married father of four who had campaigned on "family values", said on Friday he had the support of his colleagues to continue.
But Turnbull responded on Thursday by banning his ministers from having sex with staff.
Joyce said his party would support the PM's new code of conduct banning sex with staff and "we will do our best endeavours to see it through", but added it would "create vast fodder" for the media.