Europe’s animal farming sector has exceeded safe bounds for greenhouse gas emissions, nutrient flows and biodiversity loss, and urgently needs to be scaled back, according to a major report.

Pressure on livestock farmers is set to intensify this century as global population and income growth raises demand for meat-based products beyond the planet’s capacity to supply it.

The paper’s co-author, Professor Allan Buckwell, endorses a Greenpeace call for halving meat and dairy production by 2050, and his report’s broadside is squarely aimed at the heart of the EU’s policy establishment.

Launching the report, the EU’s former environment commissioner Janez Potocnik said: “Unless policymakers face up to this now, livestock farmers will pay the price of their inactivity. ‘Protecting the status quo’ is providing a disservice to the sector.”

The study calls for the European commission to urgently set up a formal inquiry mandated to propose measures – including taxes and subsidies – that “discourage livestock products harmful to health, climate or the environment”.

Livestock has the world’s largest land footprint and is growing fast, with close to 80% of the planet’s agricultural land now used for grazing and animal feed production, even though meat delivers just 18% of our calories.

Europeans already eat more than twice as much meat as national dietary authorities recommend – far beyond a “safe operating space” within environmental limits, says the Rise foundation study.

As a result, huge sectoral “adjustments” will be needed by 2050 to rebalance the sector, including a 74% drop in greenhouse gas emissions and a 60% cut in nitrate-based fertiliser use, it finds.

Long before then, policymakers, farmers and society as a whole face “deeply uncomfortable choices”, according to Buckwell.

“We’re talking about fewer meat meals, less meat portions and moving to flexitarian diets without being dogmatic about it,” he said. “There is a role for softer public health messaging but harder messages are necessary too.”

Such a transformation “won’t happen spontaneously”, he added. “It requires strong signals from government so the policy proposal must include measures to discourage consumption of livestock products harmful to public health and the environment.”

Buckwell called for targeted taxes on harmful practices, with subsidised meat for low-income consumers, and a realignment of funding regimes to advise, retrain and hire more farmers for work in rural landscape management and animal welfare.

The hope is that consumers will eventually pay more for high quality meat produced in environmentally safe conditions, where countryside protection and animal welfare have been guaranteed.

The study follows angry condemnation of the EU’s recent common agricultural policy reform, which ignored a growing clamour for moves to more sustainable food systems.

Addressing the launch in a video message, the EU’s agriculture commissioner, Phil Hogan – who dismissed the sector’s emissions footprint earlier this year – said that he too wanted it to become “smarter, greener and cleaner, and do so fast”.

But his claim that more farm efficiency was the answer was slammed as “inherently contradictory” by BirdLife Europe’s policy chief, Ariel Brunner. The most sustainable farms are often less “efficient” in narrow terms of profit and loss, he argued, unless broader questions of energy and nutrition are considered.

One of the largest barriers to this sustainable food vision is Europe’s farmers themselves, still reeling from the financial blow dealt by this year’s drought.

Liam MacHale, the secretary-general of the Irish Farmers’ Association, told the Guardian that farmers were “an easy target” for environmentalists.

“Don’t single out our sector,” he warned the report’s authors. “Look at greenhouse gas emissions. Agriculture is blamed but look at consumer behaviour in the transport sector. They need to fly abroad to relax [despite] the emissions associated with that. The airlines are not being closed down, yet you’re talking about possibly eliminating the livestock sector.”

Buckwell told the Guardian he envisaged a contraction of the sector of between 40%-50%. “We have to contract consumption by roughly half to come within the safe operating space – a big change, in other words.”