Farmers are finding preparing for Brexit as disruptive as a major disease outbreak, and food companies are in danger of moving out of the UK or scaling back their investment, a farming leader has warned.

Minette Batters, president of the National Farmers’ Union, said: “Millions are being spent every day in no-deal planning and contingency plans for the food industry. Businesses are having to invest so much money to protect us from an inept parliament. This will break some businesses.”

She added: “It is like disease crisis management, but we don’t even know what we are going into.” Asked whether a disorderly Brexit could have as much impact on farming as the foot and mouth epidemic of 2001, she said it was not yet possible to tell. “Who knows? It depends on what the government and the EU do.”

While the decision by the carmaker Nissan to scale back UK investment hit the headlines and caused widespread concern, food companies have received relatively little attention. Batters pointed out that food was the UK’s biggest manufacturing sector, but many of the key companies are foreign-owned. For instance, the animal feed industry is dominated by Irish companies, while Danish and Dutch firms play a key role in pork.

Those companies and others could decide to move elsewhere in Europe, she said. “Food businesses are here for the time being, but they do not have to have their business in Britain. Why would you have a business here? The government is being really naive in how they are dealing with this – [these companies] don’t have to stay here.”

Concerns among farmers and the food supply chain are less obvious than in concentrated industries such as car-making because they are more diverse and spread across the country, but the businesses involved face just as much difficulty.

Batters called on the EU to put in place emergency measures that would ensure the UK’s farm and food products were treated in the short term as compliant with EU standards even in the event of no deal.

After Brexit, she said, the same high standards should be enshrined in UK legislation rather than left up for grabs in trade deal negotiations.

“We believe in animal welfare and the future of the environment and food safety. We must agree a black and white policy statement that is going to be in future free trade agreements,” she said.

This weekend marks the start of the Big Farmland Bird Count, carrying on until 17 February. Batters is encouraging farmers across the country to take part to highlight the importance of farms to the conservation of the UK’s landscape. ’Her own farm in Wiltshire is the habitat for dozens of bird species including heron, teal, cormorants, mallard and swans. Mistle thrush make their home in the mistletoe that grows thickly on 400-year old lime trees near the farmhouse.

Peter Thompson, biodiversity advisor at the Game and Wildlife Conservation Trust, which organises the annual count, said that if farmers gave even 5% of their land over to conservation, it could make a big difference.

“Many farmers already do a lot, such as supplemental feeding – sprinkling grain and seeds for birds to eat during the hungry gap from January to April,” he said. “Intensive farming can go alongside nature if farmers are aware of how they can improve and provide habitats for birds, wildlife, insects and wildflowers.”

There have been precipitous declines in farmland birds in recent decades, mostly as the result of intensive farming. After Brexit, the government’s agriculture bill will set up a system of environmental land management contracts under which farmers will receive taxpayer subsidies if they agree measures to safeguard biodiversity and protect waterways and other important natural features.