Senator McMahon is a member of the Country Liberal Party but she had sat in the Nationals party room.
"Sam remains part of the government and that's very very important," Mr Joyce, the deputy prime minister and Nationals leader told Sky News' Sunday Agenda program.
"We are talking about something very close to the end of parliament before we go to the election. I don't think this is a dramatic issue."
But Senator McMahon's decision does come at a time when polls are showing the government and Prime Minister Scott Morrison are losing popularity.
Mr Joyce threw his support behind Mr Morrison.
"What other prime minister has had to deal with a pandemic," he said.
"I think the Australian people ultimately are going to have to make a choice between secure management ... and Mr Albanese who is one person in Mackay, another person Melbourne, another person Gladstone, another person in Grayndler.
"In between times he is just whingeing and whining commentary about how terrible we all are ... I want to hear his positive message."
Mr Albanese did his best to do just that in an interview on the ABC's Insiders program, announcing that aged care funding will be increased if Labor wins the election which is due to be held by May.
He also believes that every budget should consider improving the JobSeeker dole payment rate.
At the same time, Labor wants to ensure critical medical supplies are manufactured in Australia.
"One of the lessons of this pandemic is we need to be more self-reliant," Mr Albanese said.
A Labor government would instruct the $15 billion National Reconstruction Fund to make medical technology a top priority.
"During this pandemic, we haven't had enough PPE equipment, we haven't had enough ventilators, we haven't been able to produce rapid antigen tests and we are still not producing mRNA vaccines," he said.
Mr Albanese also thinks budget repair should have started before now.
The Labor leader said it was entirely appropriate to spend and to stimulate the economy during the pandemic, just as it was during the global financial crisis.
"What's not appropriate is the pork-barrelling and waste that we've seen," he said.
Something like $20 billion was wasted on the JobKeeper program where money went to businesses that didn't need it and instead increased their profits, Mr Albanese said.
He said there was $16 billion on the government's books for decisions taken but not announced for political decisions.
"They won't tell taxpayers what it will be spent on," Mr Albanese said.
"That sort of reckless abuse of taxpayers' funds has to stop and we would stop it."
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