Defence Minister Peter Dutton told Question Time Mr Joyce had been identified as a possible contact of a COVID-19 case after attending a function.
However, the Nationals leader has since returned to the House.
Mr Dutton said no other federal representatives were believed to be in a similar situation.
All NSW MPs were issued with a “stay put” directive after it was revealed NSW Agriculture Minister Adam Marshall contracted the virus.
NSW Premier Gladys Berejiklian and Health Minister Brad Hazzard have both been released from isolation after testing negative for the virus.
The agriculture minister dined with Nationals MPs Ben Franklin, Trevor Khan and Steph Cooke at Christo’s Pizzeria eatery on Monday.
A message from government whip Adam Crouch just after 9am this morning advised ministers to “stay put” and not move until they receive further updates following the positive diagnosis.
“If you are currently in Parliament House, remain in Parliament House,” the message read.
“If you are not in Parliament House, remain where you are.”
Ms Berejiklian confirmed at a press conference she had been categorised as a casual contact and isolated until she returned a negative test result today.
She said she had not had any contact with Mr Marshall.
“He has been interviewed and he had zero contact with me and others. I was interviewed and had zero contact,” she said.
“I was there for a short time, addressed the crowd and didn’t have contact with him whatsoever.”
She has received both doses of the AstraZeneca vaccine.
Mr Hazzard tweeted that he too had returned a negative result and was released from isolation as a casual contact.
Mr Marshall returned a positive test result this morning and is currently asymptomatic.
“This morning just after 8am, I was formally advised by NSW Health that I had returned a positive test for COVID-19,” Mr Marshall said in a statement.
NSW Health informed him via text message late on Tuesday night that he attended a “close contact venue” on Monday evening and needed to get tested.
Mr Marshall said he was “doing fine” and would continue to follow health advice.
“To everyone who has contacted me this morning, thank you for your thoughts and well wishes – I’m doing fine and will continue to strictly follow the advice of health authorities,” he said.
“To our wonderful NSW Health staff, who continue to do an amazing job in these challenging times, thank you for your support and efforts keeping all of us safe and well.”
Earlier this morning, Parliament whips sent notes to members telling them not to bring in staff due to the positive case and other MPs in isolation.
Earlier, it was indicated that both houses will still sit today with numbers and time in parliament cut to a minimum, however that now appears up in the air.
Mr Hazzard said he was “quite confident” NSW would have a “proportionate response” to the current COVID-19 outbreak.
“I feel confident that we will continue to manage it carefully,” Mr Hazzard said.
“The restrictions that were put in place are proportionate, they are sensible.
“But certainly we have never, ever before said wear masks basically everywhere except your home.”