Lorries carrying perishable food and plants from the EU are being held for up to 20 hours at the UK’s busiest Brexit border post as failures with the government’s IT systems delay imports entering Britain.

Businesses have described the government’s new border control checks as a “disaster” after IT outages led to lorries carrying meat, cheese and cut flowers being held for long periods, reducing the shelf life of their goods and prompting retailers to reject some orders.

The worst disruption was last weekend, with dozens of lorries being held at the government’s control post serving Dover and the Channel tunnel for periods of between eight and 20 hours after the IT system that registers goods went down.

Ministers brought in physical checks on animal and plant products from the EU at the start of this month as part of its post-Brexit import regime.

However, since their introduction, problems with the government’s Automatic Licence Verification System (ALVS) have led to an increasing number of lorries being held at border posts for many hours while the checking of documents is carried out manually.

The Guardian spoke to several importers and customs agents whose lorries were stopped at the Sevington post in Ashford, Kent, over the weekend after the IT system failed.

One company that imports Italian goods said that 18 of the 23 lorries that came through the Port of Dover were sent to Sevington, with some having to wait between nine and 20 hours before being released.

In one case, a lorry entered the Department for Environment, Food and Rural Affairs (Defra) facility at 6am on Sunday, and was only able to leave at 2am Monday morning.

A manager at the company, who preferred not to be named, said: “We were expecting maximum hold-ups of four hours, and, if they weren’t checked by then, they would be released. This is a lot longer.”

The government confirmed that a technical issue had affected Defra’s digital services on Saturday, which had affected the ALVS.

To overcome the problems, importers had to manually submit documents to border officials to be checked before they could be released. Defra said there had been no significant delays to border checks.

The managing director of a Polish transport company said the weekend had been a “disaster” for importers, resulting in a lot of angry customers. “There was huge disorder, and a lack of information about the status of the lorries,” he said.

Mariusz, a driver who had been held at Sevington for more than eight hours, told the Guardian that the delay had led to him being late for a drop-off. He said there were 25 other lorries stuck at Sevington, some for 15 hours, with little information being given on when they would be released.

Other custom agents and importers complained that it was impossible to get through to Defra officials on the phone on Sunday.

A representative of a company that sends 70 lorries a week to the UK, said it had seen 40 vehicles sent to Sevington last week for document checks, with the hold-ups leading to some customers rejecting deliveries.

He said: “We have fresh products from Poland and eastern Europe, which can take two to three days to transport to the UK. If there is another delay of a day or two, it’s really too late to sell them to final customers.”

Traders said this was the latest in a list of problems with the government’s IT systems since the border checks were brought in on 30 April, with the ALVS being down on two other occasions.

Nigel Jenney, the chief executive of the Fresh Produce Consortium, said: “There’s been several incidents like this in the last two weeks, and several much more minor issues. There is a huge concern factor. This is causing not just huge disruption, but it’s a huge cost for the sector.”

A Defra spokesperson said: “A power outage over the weekend affected one of the systems required to process imports. For the majority of vehicles at the border there were no significant delays, but we immediately activated contingency arrangements for affected vehicles, working alongside HMRC and Border Force.

“We are working at pace to resolve the issue and expect that systems will be returning to normal functioning soon. Since the introduction of checks, our teams have been working closely with traders to ensure checks are completed efficiently and swiftly.”