The sticking point for Australia has been agriculture, as it pushes for greater market access for beef and sheep, with talks down to individual tonnage for quotas.
Senator Farrell will meet with EU trade commissioner Maros Sefcovic and agriculture commissioner Christophe Hansen.
"As I have clearly and consistently said, any deal must be in Australia's interests and include new, commercially meaningful market access for Australian agriculture," Senator Farrell said pre-departure on Wednesday.
"I don't do bad deals."
European Commission president Ursula von der Leyen is expected to arrive in Australia in coming weeks, which adds pressure to have the deal ready to sign during her trip.
It's hoped the trade ministers' meeting clears the path for the agreement to be signed.
Australia had initially pushed for more than 30,000 tonnes of beef, while Europe tried to whittle the quota down to protect domestic farmers who oppose the market being flooded with more meat, therefore eating into their income.
However, negotiators are still at an impasse over some import restrictions.
Even though other free trade deals Europe has signed, such as with Canada and New Zealand, allocated tens of thousands of tonnes of tariff-free meat, they haven't been able to use the vast majority due to Europe's strict import controls.
European conditions span deforestation regulations for farms, hormone-free growth and transport requirements.
The issue of geographical indicators - when Australian producers use names of foods that come from specific regions, such as prosecco and feta - had also been a point of contention, as Europe pushes to end the use of particular product names.
There has been a resolution on more than 400 product names, including grandfathering, which is when current producers have leeway but future market entrants can't use the names.
But four remain at gridlock: prosecco, feta, parmesan and pecorino.
Brussels has also sought access to Australian critical minerals, but an initial proposal for exclusive access through a dual-pricing mechanism was rejected by Australia.
Dual pricing sets different prices for domestic and international markets.
Resources Minister Madeleine King argued accepting this would impede Australia's ability to set policy in the sector, including implementing mechanisms to prop up local industry.
The trade minister and the treasurer are also in contact over how much of Australia's luxury car tax could be foregone as part of the agreement, which was put on the table initially to get the Germans over the line.
There are also discussions about skilled worker visas, with Europe pushing for a full waiver of labour market testing, an absolute non-starter for the Labor government.
Labour market testing is a requirement for specific visa categories that require employers to prove they attempted to hire a local worker before employing foreign labour.
Negotiations are now centred on facilitating temporary entry for skilled workers, professionals, investors and researchers, but any changes wouldn't allow EU citizens to work freely and live in Australia, and vice versa.
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