The UK has strict laws on animal transportation and it is forbidden to travel with cattle for more than 14 hours without stopping for food or water.
However, in parts of Australia it is legal to transport cattle for up to 48 hours without eating and drinking.
Campaigners have complained the trade deal would make it easier for Australia to export cheap meat to the UK market at the expense of livestock welfare.
Compassion in World Farming called the deal “completely unacceptable” while the RSPCA warned it paves the way for future deals that permit “poor animal welfare”.
James West, senior policy manager at Compassion in World Farming, told The Independent: “We should not be undermining improvements in UK standards by importing products from animals that have suffered even more elsewhere.”
David Bowles of the RSPCA said: “The UK has promised to lead the world on animal welfare – but this is just telling future trade partners that poor animal welfare is no impediment to a trade deal.
“With the UK government seeking to sign trade deals as quickly as possible, we’re likely to come under pressure to lower standards or let in lower quality products.”
The campaigners said the move contradicts a promise made in the Kept Animals Bills, which pledged a “manifesto commitment to end excessively long journeys for slaughter and fattening”.
It added: “Now we have left the EU, we have the opportunity to look at alternative methods to better protect animal welfare during transport.”
The free trade deal, which was agreed in principle last year, is expected to be ratified in the final three months of 2021.
The deal means British products such as cars, Scotch whisky, biscuits and ceramics will be cheaper to sell to Australia, the UK Government said.
Meanwhile, it will eliminate tariffs on popular Australian products such as Jacob’s Creek, Hardys wines and swimwear.
Some UK industry leaders raised concerns about potential compromises to food standards while farmers worry they could be undercut by cut-price imports.
The High Commissioner for Australia George Brandis has previously justified longer journeys by telling MPs that Brahman are “durable beasts”.
He added: “The cattle there are Brahman cattle, which is a completely different breed from the type you have in the United Kingdom. They are bred for dry conditions and they are very durable beasts.
“Please let us not use this 48-hour figure, because it is extremely rare. It applies only to cattle of a kind, durability and robustness that you do not have in the United Kingdom. It is misleading to think that is an Australian standard.”
The Department for Food, Environment and Rural Affairs has been approached for comment.