The Government’s fiscal watchdog has issued a scathing assessment of the new border control system, highlighting its partial implementation three years post-Brexit transition.

In a report released earlier this week titled ‘Implementing an Effective Trade Border,’ the National Audit Office (NAO) criticised the Government’s Border Target Operating Model (BTOM) for creating uncertainty, increasing risk, and adding costs to the supply chain.

Initially, the government planned to implement a full import control regime on January 1, 2021. However, the NAO found that “more than three years after the transition period ended, full import controls are still not in place. Moreover, the model’s operation has yet to be tested, and the government might struggle to consistently apply controls as they are gradually introduced.”

The report highlighted that the UK has faced heightened biosecurity risks due to the phased introduction of full import controls.

“Departments have assessed that biosecurity risk to the UK has increased since the end of the transition period,” the report stated. “Losing access to EU surveillance and alert systems has also diminished the UK’s awareness of impending threats.”

The NAO emphasized that the recent lack of requirement for Export Health Certificates for goods arriving from the EU could have complicated tracking the source of an outbreak if one had occurred.

“The Animal and Plant Health Agency has been conducting checks on high-risk goods at their destinations rather than at the border. Due to the geographic spread of locations, it has not been able to perform all required checks under the existing regime, thereby increasing biosecurity risk,” the report explained.

The report also mentioned the government’s plan to implement new import controls “flexibly” while Port Health Authorities and local authorities recruit and train staff and while traders adapt.

“While the government plans to scale up checks nationally, there will likely be a period where different levels of control and checking are applied at different ports. Stakeholders expressed concerns that this could shift trade flows to the entry points with the least resistance,” it warned.

Wasted Spending

The report noted that the government expects to spend at least £4.7 billion to implement new border arrangements related to the EU exit and enhance border performance.

“The government’s new border target operating model should reduce costs for traders compared to its initial plans,” the NAO report stated.

“However, repeated delays in implementing controls have caused ongoing uncertainty and increased risk, leading to unnecessary costs for the government and border stakeholders.

“These issues could have been avoided if the government had established a clearer vision for border operations from the start and adopted a more strategic and planned approach to implementation.”

The report pointed out that changes in the introduction of import controls led to unnecessary expenditures on infrastructure and staff.

For instance, the government spent £62 million on sites at Dover White Cliffs and Dover Bastion Point, only to later determine they were unnecessary under the new risk-based import control regime for SPS goods, which reduced the volume of goods needing checks.

HMRC also spent £258 million between 2020-21 and 2023-24 on eight temporary border facilities to handle additional demand that did not fully materialize.


The government’s 2025 UK Border Strategy proposed using technology and data to facilitate legitimate trade while identifying risky individuals and goods, a strategy supported by most stakeholders.

“However, there is no timetable for achieving these ambitions, and the extended phasing of full import controls has slowed progress on other elements of the strategy,” the NAO report concluded.

It acknowledged that the new border control regime is a significant challenge, involving several large programs across multiple departments and external stakeholders.

“To improve its chances of success, the government needs strong mechanisms for delivery and accountability, a more realistic approach to digital transformation, and methods to assess and report on border performance for ongoing improvement,” the NAO said.

The report reinforces industry concerns about the current state of border controls, particularly the decision to cut funding for illegal meat import checks at the Port of Dover to fund the new BTOM.

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