But Turnbull said the scandal had prompted overdue changes to ministerial conduct rules, and announced new standards broadly similar to a ban on relationships between lawmakers and staffers adopted last week by U.S Congress.
Mr Turnbull was scathing in his assessment of Mr Joyce's personal dramas.
Prime Minister Malcolm Turnbull accused Barnaby Joyce of making a "shocking error of judgment" by having an office affair which had hurt his wife, his four daughters and his new partner who is due to give birth in April. "In doing so, he has said off a world of woe for those women and appalled all of us".
He said that whatever people might have turned a blind eye to in years past, in 2018 it was not acceptable for a minister to have a sexual relationship with someone who worked for them.
And things were set to get even more embarrassing next week when Turnbull jets off to the United States, leaving Joyce to perform the role of Acting Prime Minister.
Foreign Minister Julie Bishop, as deputy Liberal leader, would normally step in if Joyce was unavailable.
Problems have been piling up for Barnaby Joyce since his relationship with former staffer Vikki Campion was exposed.
Mr Joyce's affair has spurred a debate in Australia about what parts of a parliamentarian's life are private and should be off-limits to media reporting.
Labor senator Kimberley Kitching on Wednesday tabled a notice of motion calling for the details of Mr Joyce and Ms Campion's "special goal travel" and any worldwide flights. Labor leader Bill Shorten asked.
For his part, Mr. Joyce is taking time off to spend more time with his family and pregnant partner after the intense public focus that followed the initial revelations by the Sydney Daily Telegraph newspaper.
'The most pathetic speech Malcolm Turnbull has ever given, ' a social media user wrote.
The opposition Labor Party had hoped disaffected lawmakers in Barnaby Joyce's own Nationals party would back their motion, but coalition lawmakers in the House of Representatives held firm and defeated it 73 to 70. But she will also be travelling, which means Senate leader Mathias Cormann will take the position.
The issue of Mr Joyce moving from a central role in a controversy to the job of Acting Prime Minister was discussed over a week, with the Deputy Prime Minister refusing to budge. "And everybody knows that no good comes of it", he said.
Mr Joyce told Parliament he was not aware his administration had made a $5000 payment to Armidale businessman Greg Maguire, who had given the Nationals leader free accommodation when Mr Joyce's marriage collapsed.
"Ministers should be very conscious that their spouses and children sacrifice a great deal so they can carry on their political career and their families deserve honour and respect", he said.
"It's been an extraordinarily hard time for the. party and clearly for Barnaby Joyce and his family and for the government", Anthony told reporters.