The UK’s fruit and flower growers face an “existential threat” from new post-Brexit border checks that could damage business and affect next year’s crops, the country’s biggest farming body has said.

The National Farmers’ Union (NFU) warned that changes to import rules in April, which will impose checks at the border for nearly all young plants coming into the country, could cause long delays and result in plants being damaged or destroyed.

Martin Emmett, the NFU’s chair of the horticulture and potatoes board, said: “There is a concern that border control points can pose an existential threat to horticultural businesses in this country.”

Emmett, whose company Farplants grows about £20m of product, with just over half starting life in the EU, said: “Having unusable deliveries is what terrifies growers, and any unnecessary delays could result in stock destruction, and that ultimately impacts on businesses in the most profound way imaginable.”

UK growers are reliant on the EU for young plants that start life in countries such as the Netherlands before being imported into the UK for planting.

Most soft fruit plants, including strawberries and raspberries, are imported as young plants, while significant numbers of tomatoes, fruit trees and nursery plants also start life in European countries equipped with large greenhouses and better conditions.

Under current rules, imported plants are held at nurseries and farms in controlled conditions before some are checked by government inspectors, with checks often prioritised based on risk.

However, under new rules scheduled to come in on 30 April, the government intends to check 100% of consignments coming through the new border posts.

This has led to widespread discontent among growers, who have concerns about the ability of these border posts to handle this volume of imports.

They believe delays and conditions at the new posts could lead to crucial plant imports being damaged or destroyed, and threaten crops for the coming year.

The Guardian has spoken to bodies that represent fruit and flower growers which have echoed the NFU’s concerns, including the Horticultural Trades Association (HTA), British Apples and Pears, the British Tomato Growers’ Association and British Berry Growers (BBG).

Nick Marston, the chair of BBG, said the border checks caused great concerns for the UK strawberry industry, which is heavily reliant on EU young plant imports, having brought in about 100m plants last year.

He said: “We are very concerned about the government’s ability to process all those incoming plants on a timely basis, and the losses to growers that could ensue as a result of delays, which could add up to hundreds of thousands of pounds.”

The HTA said it was yet to be reassured that the border posts were ready, and had serious concerns that they were planned for the spring – the peak season for the sector.

The checks make up part of a new post-Brexit border regime, known as Border Target Operating Model (BTOM), which has already been delayed five times.

This will require European importers to provide health certificates for “medium and high-risk” animal and plant products from 31 January, with physical inspections of these goods due to start at the end of April. Nearly all young plants are considered high risk.

The government has said the border strategy was to “protect the UK against biosecurity threats”, and the new controls would use “Brexit freedoms to simplify import controls on goods from across the globe”.

Growers groups said that while they were supportive of the government’s biosecurity aims, some were unconvinced that the posts, which could involve different plants unloaded in depots side-by-side, would achieve this aim.

Robert James, the co-chair of the Tomato Growers’ Association technical committee, said the border posts lacked the same controlled conditions seen on farms.

James said: “We’re introducing a really significant point of infection, or introduction of pests, which could put growers’ crops at massive financial risk of crop failure.”

Last month, Dutch flower sellers called for delays to the checks, warning it was worried its products could suffer “substantial damages and losses” at the border.

The new border control posts have been established near some of the UK’s biggest ports, including a new major border post at Sevington, about 20 miles from Dover.

The government is hoping to trial a system where growers can become de facto border posts, but these require large amounts of investment from companies.

The NFU is calling for the government to allow plants to bypass these posts with “place of destination” checks, while adopting a more risk-based approach to reduce the number of checks.

A Department for Environment, Food and Rural Affairs spokesperson said: “We have introduced these new import controls in phases to support businesses and ensure efficient trade of plants is maintained between the EU and Great Britain.

“The current ‘places of destination’ scheme was always designed to be a temporary measure until inspections commenced at border control posts.

“The controls that the new model introduces play a vital role in keeping the UK safe, protecting our food supply chains and farming sector from damaging disease outbreaks.”