The pros and cons for farming of closer EU alignment

Progress towards establishing a common sanitary and phytosanitary agreement with the EU – part of the government’s “reset” initiative – is gathering momentum.

Negotiations started in earnest in January, and meetings between both sides’ officials are said to be taking place on a weekly basis, to try and work through the mass of regulation that will need to be changed in the quest for a smoother trading environment.

Defra also issued a six-week “call for information” in early March of this year, seeking feedback from UK stakeholders on what impacts they might feel from dynamic alignment with EU rules, and what support they might need in the process.

But what exactly is a sanitary and phytosanitary (SPS) agreement and what difference might it make?

Background and timetable

The SPS is part of a wider package agreed under a “strategic partnership” signed by the UK and EU in May 2025.

Other elements include a “youth experience scheme” and “emissions trading system”, and it is understood that the EU wants to sign off all three together, rather than prioritise the SPS alone.

The SPS element covers the trade, production and movement of plants, animals and their products between Great Britain and the EU, seeking to ease the paperwork and controls that are currently required.

But it goes further than that, also covering food and feed safety, nutritional supplements, food labelling, and organic production standards, as well as the regulation of pesticides, biocides, veterinary medicines, and genetically modified organisms.

Aligning with the EU rulebook will remove the need for reams of costly red tape for traders, such as export health certificates, phytosanitary certificates, and organic inspection certificates, not to mention the time-consuming border checks (admittedly more of an issue for UK goods entering the EU than those coming the other way).

Closer alignment with the EU would also free up trade between GB and Northern Ireland, while continued application of the Windsor Framework would enable Northern Ireland to maintain its special access to the EU single market (principally the Republic of Ireland).

There is also scope for the UK to agree certain exemptions from the EU rulebook, so long as they do not result in lower standards in the UK or disadvantage EU goods entering the UK.

Timing

While negotiations are said to be happening at pace, the exact timeframe remains unclear. The government insists it “won’t provide a running commentary on the talks”, but the declared intention is for the SPS agreement to be signed off by the next UK-EU summit.

There is no agreed date for that, but it is expected this summer, with full implementation in mid-2027.

Closer alignment is likely to come at a cost, with the UK expected to make “an appropriate financial contribution” towards EU coffers.

Contrary to some opposition claims, the UK would be offered a degree of influence on future EU standard setting, but would not have voting rights.

And, while there will be an arbitration systems, ultimately any disputes between the two sides would be determined in the European Court of Justice.

What are the expected benefits?

There is no doubt that government and exporters see tremendous upside from a successful negotiation.

In a lecture to business leaders last month, chancellor Rachel Reeves talked about a “shared burden reduction ambition” stating that the UK had committed to a 25% cut in associated red tape by the end of the current parliament – worth an estimated £6bn for 500,000 businesses affected.

At a more granular level, Defra says an SPS deal would save food exporting businesses up to £200 per consignment by no longer needing Export Health Certificates, £25 a shot from the end of phytosanitary certificates, and £128 in reduced EU inspection fees.

Sampling is said to cost approximately £1,200 for a load of cheese or beef, and £440 for a consignment of apples, while queuing times at points of entry can add £200 in extra driver hours.

In total, some 1.08m export health certificates have been issued for trade with the EU and Northern Ireland since 2023, says the Cabinet Office, at a cost to exporters of more than £100m.

A government spokesman says, as well as cutting costs and delivering for the economy (see “The government line” below), an SPS agreement will go a long way to recouping some of the £4bn (22%) of lost exports to the EU since 2018.

The AHDB agrees. “The EU market is and will remain our key trading partner due to our proximity to market and established supply chains,” says AHDB head of economics Sarah Baker.

“Any agreement that lowers trade friction, smoothing trade between the UK and the EU, would be good news for UK agricultural exporters.”

Dairy and red meat suppliers would be the primary beneficiaries, with 80-95% of beef, lamb and cheese exports all heading to the EU, according to the AHDB.

An SPS deal should also trigger the resumption of trade in currently banned British products, such as seed potatoes and sausages, and re-open the trade of live animals for breeding.

There could also be biosecurity advantages, as the UK would gain access to EU databases about disease spread and control, increasing our resilience in the case of any emerging threat.

What are the stumbling blocks with an SPS agreement?

Despite significant potential benefits, there are numerous fears about the effect an SPS deal could have on UK agriculture. The key ones include:

Plant protection products

Research by consultants Andersons for plant protection body CropLife explains that, since the UK officially left the EU five years ago, the systems for approving active ingredients have diverged.

Four new products – bixlozone, cinmethylin, isoflucypram and pydiflumetofen – have been approved for use in GB that are not currently available in Europe, while a further 14 actives are still approved in the UK, but have already been banned or are being phased out in the EU.

The Anderson’s analysis suggests that, in a worst case scenario where the UK aligns with EU rules overnight, the immediate loss of all those products would lead to a significant yield drop to GB cereal growers, plus additional costs. This could mean a 3-6% fall in gross value added for UK crop production, knocking £500m-£800m off industry profit.

The NFU also points out that the UK might have to follow EU glyphosate rules under an SPS agreement, which prohibit its pre-harvest use as a desiccant and restricts total use in agriculture to 1.44kg/ha a year.

It is also concerned that some crops that have already been planted at the time of alignment, could become technically unsaleable if they have been grown using plant protection products (PPPs) that are already banned in the EU.

And it points to significant costs if those PPPs sitting in farm stores have to be destroyed.

“The NFU is deeply concerned that a single date for dynamic alignment with EU plant health and PPP regulations would pose significant challenges for the industry,” it says in a briefing document to MPs.

“The industry is likely to be disrupted and potentially damaged if businesses are not afforded sufficient time for adjustment.”

Conversely, there could be some potential benefits to realignment for British farmers and growers, with more than 20 new active substances, mainly biopesticides, that are not licensed in GB becoming available through a process of “mutual recognition”.

Precision breeding

The UK is ahead of the curve in terms of precision breeding – especially for plants – with legislation passed in 2023 and effective from 2025, paving the way for the use of gene editing in developing more resilient crops. Field trials are getting under way this spring, including a crop of high lipid barley.

The EU seems to be heading in a similar direction, having agreed its own legal framework for “new genomic techniques” – but it is not there yet.

The potential problem this might cause the domestic plant-breeding sector in the case of alignment with the EU were spelled out in a report from the cross-party Environment, Food and Rural Affairs (Efra) committee, published in February.

“The EU’s forthcoming new genomic technology framework could take several years to be finalised, and waiting for alignment between the EU and UK on precision breeding would undermine England’s ‘first-mover’ advantage and stall the development and release of precision bred organisms,” it says.

Committee chairman Sir Alistair Carmichael says regulatory alignment must not squander the benefits reaped from the UK’s scientific innovations with precision breeding, and government should actively progress regulatory procedures to bring precision-bred plants to market.

Fortunately, Defra has already indicated that this is indeed a priority in its negotiations with Brussels, though success is far from guaranteed.

Bovine TB

With the current government well on the way to ending all culling of badgers as a means to contain the spread of bovine TB in cattle, the emphasis is shifting to vaccination strategies.

However, EU legislation currently prohibits the use of vaccines against TB infection in cattle, and the NFU is deeply concerned that, with EU alignment, that could apply to the UK too.

There is also a fear that if the UK were to press on regardless, there could well be trade issues for both meat and dairy, as the EU might not accept products from vaccinated animals.

The NFU is therefore urging the government to protect the ability to vaccinate cattle against TB, and resolve any trade implications as part of the SPS agreement.

Organic standards

A major area of divergence is organic food production, especially since new regulations came into force in the EU in 2022.

While the new EU rules align very closely with GB rules for most organic crop and livestock production, this is not the case for poultry, which remains especially vulnerable.

There are two particular issues.

For laying hens, current GB rules allow egg producers to source their point of lay pullets (up to 18 weeks old) from non-organic rearers. Indeed, there are no facilities for organic pullet rearing in GB anyway.

However, the new EU rules stipulate all birds must be raised fully organically from three-days old onwards.

Failure to secure a derogation could seriously damage the domestic organic egg sector.

British Free Range Egg Producers Association head of strategy Gary Ford said: “We are very concerned that the changes to GB organic standards will make organic egg production increasingly unviable, leading to an increase in imports.”

The second concern – which also affects pigs under 35kg – is that GB rules currently allow organic layers and broilers to receive up to 5% non-organic feed in their rations, when sufficient organic protein (typically maize gluten) is not available.

While the EU has a similar derogation, this is due to expire in December 2026 and forced realignment for GB producers from mid-2027 could impact bird welfare and productivity, and even lead organic poultry producers to quit the sector.

Other concerns

The aforementioned concerns are not the only ones. The NFU has also raised potential issues relating to:

• Antimicrobial use. EU rules limit the preventative use of antimicrobials to single animals only. GB rules are more lenient, allowing prophylactic use across flocks and herds in some circumstances. This could end. 
• Mycotoxin treatments. The EU has new maximum limits for mycotoxins in cereals, but these might be too restrictive for the UK environment, where conditions are very different.
• Biocides. This covers things like creosote, disinfectants and rodenticides, and was added to the list of areas covered by the SPS at a late stage. There is significant divergence between the way these products are regulated in the UK and EU.
• There is also an issue with processed animal protein (PAP).

Following a consultation last year, Defra had announced its intention to readmit porcine PAP in poultry rations, and poultry PAP in pig rations. It would also allow the use of insect protein in both pig and poultry diets.

Even though the EU already allows such practices, Defra announced in January 2026 that it would not move ahead with the necessary legislative changes until the SPS agreement is implemented.

PAP has been banned in UK feed rations since 1988 in the wake of the BSE (bovine spongiform encephalopathy) crisis, so feed manufacturers could be waiting at least another year before they can utilise this useful raw material once more.