The exchange between Richard Henderson, a media adviser to One Nation leader Pauline Hanson, and a Guardian Australia reporter was captured by TV cameras as an Adelaide press conference announcing the party's gas policy was winding down on Thursday.
As the reporter attempted to ask Senator Hanson a question about Senate pre-selection at the next federal election, Mr Henderson could be heard shouting over her.
"We're done, thank you. No, no, no. Shut up. We're done," he said as Senator Hanson and Mr Joyce began to walk away.
"Did you just say shut up?" the reporter responded.
"Yes, I did tell you to shut up," Mr Henderson said.
Moments later, Senator Hanson was caught on camera remarking to her entourage, including Mr Joyce and Mr Henderson, "Should've said, 'You're the nasty bitch'".
Mr Joyce on Friday said he had called the journalist and apologised for the "shut up" comment.
"Press conferences, (you're) on the balls of your toes, and it goes back and forth in, at times, a willing way," he told Sky News.
"I don't know, maybe that's part of the colour of it. One thing you can say about One Nation, they're never boring."
The party has had an at times strained relationship with the fourth estate, especially outlets viewed as left-leaning, since its resurgence in the polls thrust it back into the national spotlight.
ABC reporters were barred from multiple One Nation events during the party's successful campaign in the Farrer by-election earlier in May.
Senator Hanson has bristled against previous Guardian reporting about donations the party has received from mining magnate Gina Rinehart.
Mr Joyce denied One Nation was adopting tactics from the Donald Trump playbook, in which media outlets deemed unfriendly to the White House have been denied access.
"We're not the United States of America. But there are times where, obviously a journo is doing their job, but they're on an angle. They're pursuing an issue, and the politician's on their toes defending it," he said.
"I'm not purer than thou. At times I've been in press conferences where it's been rather willing, and I'll give as good as I get."
Prime Minister Anthony Albanese said the comments in Adelaide were "not appropriate", branding One Nation a party of grievance.
"They need to be held to account as well for their actions and for their policies, or lack thereof," he told reporters.
One Nation's strained relationship with the media has not impacted its popularity, at least not negatively.
A DemosAU poll published on Friday showed One Nation's primary vote share gained two percentage points to 28 per cent, ahead of Labor on 26 per cent and the coalition on 23 per cent.
The Guardian responded with "No comment" about the incident when contacted by AAP.
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