Farm animal abuses are widespread in the European Union, with pig tail docking, long-distance transport and slaughterhouse stunning all areas of immediate concern, according to a report out this week.

Intensive farms are particularly problematic, the report by the European Court of Auditors (ECA) reveals, with economic interests often trumping welfare rules. “Our audit and other reports show it’s difficult to introduce improvements on intensive farms and enforce laws,” Janusz Wojciechowski, the ECA member responsible for the report, told the Guardian.

“In intensive farming systems the risk for animal welfare is increased. When there are 100,000 pigs it is very difficult to control. Small farms are easier places to achieve high animal welfare standards.”

Inherent system failures are equally to blame. Unnaturally high number of animals living together leads “to aberrant behaviour in laying hens such as feather pecking and cannibalism, aggression and tail biting in pigs and aggression in calves”, according to the report. To address that behaviour “it is common practice to perform painful physical alterations … in particular beak trimming, tail docking, castration and teeth clipping.”

Clear evidence of pig tail docking was found on German and Romanian farms, and has been seen in many other countries by other observers, including the UK and Italy. Docking pigs’ tails has been illegal in the EU since 2001, but it is still widespread. One Romanian farm visited by the ECA had evidence of tail docking, but was simultaneously receiving EU funding to improve animal wellbeing.

Just two countries in the EU – Finland and Sweden – have properly controlled pig tail docking and provided useful ‘enrichment materials’ to ease boredom, according to the report. Dr Joanna Swabe, public affairs director for animal lobby group Humane Society International, said proper environmental enrichment, good stockmanship and simply providing straw would all help avoid mutilations.

Slaughterhouse processes were a problem too. One abattoir in France visited by the ECA team was using the less reliable back of the neck ‘occipital stunning’ on calves rather than front of head stunning. Their aim, said the report, was to reduce bone splinters in brains sold for food. Inadequate ‘waterbath’ poultry stunning (where a hen is leg-shackled to a moving line and pulled head down through electrified water) is another risk area, auditors found, as is excessive use of non-stun killing.

Using a supposedly limited EU derogation, slaughterhouses can quicken their line speeds and process more animals by skipping stunning – the part of the slaughter process which renders the animal unconscious and therefore unable to feel the actual killing. Although there is a shortage of data, non-stun derogation overuse appears to be a problem around Europe, other than the few countries where it is currently banned.

Live animal transport was also a significant issue. The French authorities had still not carried out a 2009 promise to improve their inspection procedures, while other countries, according to campaigners, were simply ignoring rest stop recommendations altogether. As a result, say campaigners, young animals that normally feed regularly they may spend 18 hours in trucks in a ship’s hold, or even more sealed up in a truck on the road.

Achingly slow response to European guidance was a regularly cited issue. Italy, for example has taken 13 years to tackle forced moulting, where hens are starved, dehydrated and deprived of light, until they lose all their feathers. The practice is used to boost egg production but, along with the suffering involved, forced moulting has been linked to salmonella infection risks. Asked if the ill treatment was now under control, Wojciechowski said “at the time of our visit to Italy, the European commission recommendation on forced moulting was still open, which might mean that this issue was still problematic.”

A significant number of the EU’s farms are also excluded from controls because they are too small: the report estimated that as many as 40% of farms fall outside the EU’s remit. Another control loophole noted in the report is the issue of ‘landless farms’ – these are often intensive pig farms, which do not use agricultural land and therefore do not benefit from Common Agricultural Policy (CAP) subsidies, setting them free from related controls and fines.

Entitled Animal Welfare in the EU: closing the gap between ambitious goals and practical implementation, the ECA report is one of about 30 published by the auditors each year, as part of their responsibility for making sure that EU funds are correctly spent. With farm subsidies accounting for about 40% of the EU’s budget, the ECA regularly examines agriculture issues. This topic, it said, was chosen because EU citizens are increasingly concerned about farming’s effects on animal welfare, and the impact on both public and animal health. ECA reports are used by various EU select committees and the parliament as a basis for policy and legislative development.

On a broader level, Wojciechowskione said the EU lacks long term agricultural vision. Given the EU’s current CAP overhaul, due to be completed by 2020 for the 2121 to 2027 period, the next two years will be pivotal. “We need a long term vision. Not for seven years, but for 30. If that vision is of intensive farming, the risks animals will be badly treated is higher.”

Describing his feelings about the welfare risks animals face in the EU, Wojciechowski said he believed the words of Mahatma Gandhi. “That the greatness of a nation can be judged by the way its animals are treated. I would say the greatness of the EU could also be judged on this.”

To address the failings identified, the report proposes multiple actions. These include improvements to enforcement, compliance, the animal welfare portion of EU rural development programmes, inspections and the penalty system. The European commission has accepted almost all the recommendations and the report will shortly be presented to the EU parliament and agriculture committee. From there, debates on legislative and other actions will follow.