Judges in the European Union have fined the UK £28 million (€32 million) as a result of its failure to impose EU rules on diesel.
There are fears in Whitehall the ruling could set a precedent over future post-Brexit dealings with the EU.
The penalty, imposed by the European Court of Justice (ECJ), is almost double what was initially recommended by advisers.
It is thought to be a warning to Northern Ireland in order to clamp down on potential rule breaking in the region.
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The fine was relative to the UK's economy as a whole, rather than that of Northern Ireland, explaining that this "would not be sufficiently dissuasive and therefore would not make it possible to achieve the aim of effectively preventing the repetition of similar infringements of EU law in the future".
The ECJ also said the fine was increased because the UK took so long to comply with the 2018 judgment.
Northern Ireland is governed by a number of EU rules for goods in order to prevent a hard border with the Republic of Ireland.
The rules are overseen by the European Commission and enforced by the European Court of Justice.
The fine came as a result of the UK's failure to implement an EU ban on the use of red diesel - which is subject to a five per cent tax rate - in private pleasure craft, such as canal boats or yachts.
The rule is meant to force boat owners to use white diesel, taxed at the full rate of fuel duty and VAT at 20 per cent.
Speaking about the ruling, prominent Brexiteer David Jones said: "The attitude is what it always was.
"The EU has always wanted to punish the UK for daring to exercise its treaty right to leave.
"Northern Ireland is the EU’s continuing leverage over the whole of the UK.
"It is exercising that leverage and will continue to do so until we take steps to break it."
Speaking to the Telegraph, he added: "This simply underlines that the Windsor Framework is a huge ball and chain that prevents the entire UK from diverging from EU regulation.