Infrastructure development for the UK’s new post-Brexit border is falling behind because of a shortage of government funding and Whitehall bureaucracy, leading British ports have warned.

As a result the government is facing calls to further delay its plans to introduce full border checks from July, or to show significant flexibility for business in the way the new rules are applied.

The issues emerged after the government decided not to increase its £200m Port Infrastructure Fund last year when it received £430m-worth of bids from UK ports for new Border Control Posts (BCPs) and other infrastructure to cope with customs controls.

In the event, the government allocated only £194m in grants to 41 ports across the UK, and then applied a 33 per cent “haircut” across the board to all successful bids, leaving many warning they would be unable to fund new infrastructure plans.

Tim Morris, chief executive of the UK Major Ports Group, which represents over 40 of the larger commercial ports in the UK, said that “inadequate” funding was forcing ports to scale back plans and making it less likely that facilities would be ready by July 1.

“We need urgent action from the government to show flexibility either on the July 1 deadline or what is required on that date. The alternative is to accept potentially serious implications for traffic flows through the ports this summer,” he said.

Richard Ballantyne, chief executive of the British Ports Association, the industry body, added there was “surprise” in the industry that the government was unwilling to release further funding.

“There is now a real danger that customs infrastructure won’t be ready by July in some ports and we’re urging ministers to take a pragmatic approach to ensure that goods can continue moving at those locations,” he said.

Among the leading ports facing shortfalls is Portsmouth, a local council-owned facility. It requested £32m in funds but received £17.1m to cover essential schemes it has estimated will cost £22.3m — leaving a £5.2m shortfall.

For now Portsmouth has been forced to scrap plans for a £7m live-animal exports BCP to service the trade in 30,000 UK breeding animals that were exported each year to Europe before Brexit. These exports are currently impossible because neither the EU nor the UK have adequate facilities to handle them.

John Royle, chief livestock adviser at the National Farmers’ Union, said it was “crucial” the lack of facilities was rectified as soon as possible, with Portsmouth and Dover both suitable candidates to support the trade. Similar facilities will need to be built in the EU.

The directors of Portsmouth International Port said plans for a post-Brexit border control post were now “well behind schedule”, blaming “delays” from the Cabinet Office and Defra, the food and agriculture ministry, according to a report submitted on Monday to Portsmouth city council.

Mike Sellers, Portsmouth International Port director, said: “We have a critical role to make sure trade is not jeopardised when new border controls come into force, however we are far from having the funds to meet even the most basic requirements.”

The report added that contractors were now indicating completion “by September 2021”, even if the £5m shortfall could be addressed, while also warning of potential staffing shortages as they looked to recruit 36 qualified full-time-equivalent staff to run the posts.

“From start to finish, this has been a frustrating process and precious time is being eaten up. The grant was underfunded from the start and its application has been inadequate, inequitable and ponderous,” the report said.

A government spokesperson said: “We are making significant preparations to ensure that they will be ready for the new procedures coming in July, including via the £200m Port Infrastructure Fund.

“Full border checks will be introduced from July 2021, and the requirement for new infrastructure is the basis on which the PIF grants have been awarded.”