Post-Brexit controls on food, plant and animal imports to Britain from the EU have come into force.

Health certificates will now be required on EU goods ranging from cut flowers, to fresh produce including meat, fruit and vegetables.

Some industry bodies raised concerns the rules could cause delays and push up costs, but others said they would help UK farmers be more competitive.

The government said its border model would “minimise burdens for traders”.

The UK left the EU exactly four years ago, but it has taken some time for the government to implement new trade rules – legally required under the Brexit agreement – for goods travelling from the EU to the UK.

Today marks the start of the changes as Britain begins reversing the free flow of such goods, which has been allowed since the creation of the EU single market in 1993. Red tape has already applied for British exporters trading in the other direction for three years.

The implementation of the changes has been delayed five times, in part to give businesses time to prepare and to reduce disruption to supply chains. The new border checks will also be phased in over the next year, with physical checks starting from 30 April.

The physical checks down the line have prompted fears of disruption to business supply chains. For example, lorries carrying goods could be stopped at ports to ensure they have the correct documentation. Concerns remain that extra checks will see import costs for businesses rise, and in turn prices for consumers.

But from Wednesday, the main change is the introduction of “export health certificates” on imports of “medium risk” animal products, as well as plant and plant products imported to Britain from the EU. The trade rules cover goods ranging from cut flowers, to cheese, fish and meats.

This means a veterinary health check will be required to be carried out in the EU on every consignment of meat, fruit and vegetable produce set to enter Britain.

While not all produce will require checks, in practice importers tend to have a mixture of goods, so most consignments will do, according to industry experts.

Controls are also being applied on goods from Ireland for the first time, but the government said its Windsor Framework means goods will move freely to and from Northern Ireland.

Ben Appleton from Liverpool Wholesale Flowers has told media that there was no need for the extra bureaucracy.

“A lot of it is already checked before it leaves anyways. On plants especially, we have plant passports in place anyways and that was all done prior to Brexit in the first place,” he said.

“Practically, it’s just more costs. That’s it, plain and simple. And it’s another set of costs that we have to pass on to the florist, [and] eventually to the people in the High Street.”

The National Farmers Union (NFU) said the livestock and dairy sectors had been pushing for a speedy implementation of import controls to safeguard UK biosecurity – protecting from imported animal and plant diseases – and competitiveness.

It said for the past three years, the delays in bringing in checks had disadvantaged UK producers as they had been subjected to EU controls, while EU exporters enjoyed “unhindered access to the UK marketplace”.

But Minette Batters, NFU president, said it was essential that border controls recognise the “different needs and nuances” of individual sectors.

She highlighted that while livestock businesses need to feel confident that border checks safeguard against disease and prevent illegal trade, delays to horticulture supply chains could result in plants being “damaged or destroyed”.

Biosecurity Minister Lord Douglas-Miller added: “The controls introduced today strike the right balance between trade and biosecurity.”

But William Bain, head of trade policy at the British Chambers of Commerce, said there were still unanswered questions around the plans.

“The government still hasn’t said what will happen if goods coming into the UK don’t have the paperwork they need.

“Will they be stopped from entering or will they be followed up afterwards? This could lead to hold-ups with deliveries if it’s not handled properly,” he said.

The Environment, Food and Rural Affairs Committee of MPs has also written a letter to Environment Secretary Steve Barclay expressing concerns over the funding for spot checks at the Port of Dover, and the location of the new facility for physical checks at Sevington, some 22 miles away from the point of entry at Dover.