EU chief Ursula von der Leyen ordered a rethink of the bloc's approach to agriculture at the start of the year in the face of widespread street protests by farmers.
Brussels has in the short term cut some red tape and eased environmental requirements for farmers in a bid to ease their ire.
But the new report is aimed at helping shape the bloc's policy on agriculture for the years to come as von der Leyen takes the helm of the EU executive for another five years.
"We will do more to protect our farmers and to make the agri-food system more resilient, more competitive, but most importantly, also more sustainable," von der Leyen said.
"We must support an agriculture that works for nature and with nature."
Among the recommendations in the report -- drawn up in consultation with farming lobby groups and environmental NGOs -- is to overhaul the EU's keystone common agricultural policy (CAP).
Negotiations on the next instalment of the CAP for 2028-2034 are set to be one of the most sensitive subjects during von der Leyen's second term in office.
"The current policy needs to be changed to meet current and future challenges," the report, which is non-binding, said.
Rather than calculating subsidies based on the size of the farms, the new system should focus more on "providing socio-economic support targeted to the farmers who need it most", it said.
Greenpeace backed the changes, saying the broad consensus on the need for reforms showed "how broken EU farming policy is".
"The EU must stop bankrolling mega-farms that pollute our rivers and drive droughts and floods, and instead help those farmers who are struggling, but making an effort to restore nature," Greenpeace EU agriculture policy director Marco Contiero said.
To help pay for the transition to greener farming practices, the report said a "Temporary Just Transition Fund" should be set up alongside the CAP.
It also said that Brussels and EU member states should step up efforts to help people switch their diets to "less resource intensive" plant-based foods rather than meat.
"It is crucial to support this trend by rebalancing towards plant-based options and helping consumers to embrace the transition," the report said.
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