DUP minister Edwin Poots breached Brexit-imposed legal obligations by ordering a halt to Irish Sea border checks, the High Court has heard.
A judge was told the inspections must be carried out due to a fundamental change in the customs relationship between Britain and Northern Ireland.
Mr Poots is being challenged for instructing Department of Agriculture, Environment and Rural Affairs (DAERA) staff to stop the checks on goods entering the region's ports.
The step taken in February this year came amid the DUP's ongoing opposition to the Northern Ireland Protocol.
Mr Poots said he had received legal advice that he could order a halt in the absence of approval for the inspections from the wider Stormont Executive.
The checks are continuing, however, under a court order imposed pending the outcome of judicial review proceedings.
A Sinn Féin member granted anonymity, another applicant named Edward Rooney, and Belfast City Council are all challenging the lawfulness of the minister's decision.
They claim implementation of the checks was allocated to Mr Poots' department, and that his subsequent decision was so significant and controversial that it required executive consent.
In court on Thursday, a barrister for the city council stressed it was seeking judicial clarity about a "government department acting inconsistently in a way that generates confusion and operational impossibilities".
Stewart Beattie KC set out how its increasing workload of carrying out some of the port inspections has led to staff levels rising from four port health officers to 32 employees.
Prior to the protocol, city council officials only dealt with a small volume of consignments from non-EU third countries.
"That designation now applies, inevitably as result of Brexit, to the United Kingdom and more particularly Great Britain," Mr Beattie said.
He disputed suggestions that council officials can continue with the checks even if they are stopped by DAERA representatives.
"That's not unlike attempting to take the egg out of an omelette, given the level and extent of interdependency between the council and the department," counsel submitted.
Mr Justice Colton was told the European Union (Withdrawal) Act and the protocol imposes a legal obligation in domestic law to apply regulations in Northern Ireland separately from Britain.
"In a nutshell, there is a requirement for checks to be carried out," Mr Beattie stressed.
"The international agreement between the European Union and the United Kingdom fundamentally alters the nature of the customs relationship between Great Britain and Northern Ireland."
It was further claimed that the terms of the protocol must be operated under "the principle of European law supremacy".
The decision to stop port checks came after Mr Poots was served with a pre-action letter by loyalist activist Jamie Bryson. In the correspondence he had contended that an absence of executive authority meant the regulations do not require the inspections to be carried out.
Ronan Lavery KC, for the unidentified Sinn Féin member involved in the case, described Mr Bryson's intervention as an "ingenious construct" which had led to the current proceedings.
Insisting there is a legal requirement for the inspections, the barrister added: "Even if we are wrong on all of that, the decision which is the subject of this challenge was clearly one which ought to have been referred to the executive.
"It is clearly significant and controversial to abandon the legal obligation."
The hearing continues.
