There is uncertainty over whether new facilities will be built at Cairnryan Port to check goods coming from the Republic of Ireland and wider EU via Northern Ireland.
The UK is finally due to start implementing post-Brexit controls on EU goods later this year.
In 2021, the Scottish government announced plans to build a new Border Control Post (BCP) at Cairnryan.
But a funding dispute with the UK government has stalled work on it.
A Scottish government spokesperson said: "Scottish ministers have asked that the full value of border infrastructure be met by the UK government, in line with promises made during the Brexit campaign.
"We have had no choice but to pause construction of the BCP until these uncertainties are resolved."
From the end of October food products being exported to Great Britain from the EU will require certification.
Physical checks of those goods is then due to begin at the end of January next year.
However, it is not certain when physical checks on goods from the Republic of Ireland entering Great Britain will begin with the UK government saying a date will be clarified later this year.
The new checks and controls will not apply to EU goods directly entering Northern Ireland due to the operation of the Northern Ireland Protocol/Windsor Framework.
The Cairnryan BCP is politically sensitive because any controls on goods which originate from the Republic of Ireland must not interfere with the free flow of goods from Northern Ireland.
The UK government has consistently promised that Northern Ireland goods will continue to have "unfettered access" to the wider UK market and intends to strengthen that promise in law later this year.
That "unfettered access" includes the commitment that Northern Ireland businesses will not have to provide official declarations of goods which are being moved from Northern Ireland to Great Britain.
This raises the question of how any officials at Cairnryan will be able to discriminate between goods from Northern Ireland and the Republic of Ireland and therefore which loads to inspect.
The movement of goods from Northern Ireland to Great Britain is based on a legal concept known as "qualifying NI goods" which states that any goods that are in free circulation in NI qualify for unfettered access.
Goods which start their journey in the EU do not qualify for unfettered access if they are moved through Northern Ireland into Great Britain for "an avoidance purpose".
However, in recent weeks, trade experts have suggested that avoidance is already happening and could increase when the new border controls are implemented.
Customs expert Dr Anna Jerzewska told the House of Lords NI Protocol subcommittee that there is "anecdotal evidence" of EU companies registering in Northern Ireland for the purpose of moving goods to Great Britain to avoid formalities and tariffs.
"We are not talking about large multinationals. We are particularly talking about small companies that are able to operate under the radar to a certain extent, with smaller movements," she said.
Peter Summerton, managing director at haulage firm McCulla Ireland, told the committee that controls on Republic of Ireland goods at other British ports like Liverpool and Holyhead would be "completely pointless" if Cairnryan was allowed to operate as an effective backdoor.
"The UK has left a clear legislative gap on how movements from Northern Ireland to GB will be controlled, should there be movement from the EU and rest of the world into Northern Ireland," he said.
Meanwhile, the Scottish government has said the UK government must "urgently clarify the policy on Northern Ireland to Great Britain trade".
A spokesperson said: "This will be crucial to understanding the impact on businesses and devolved responsibilities."
A UK government spokesperson said: "We are committed to creating a seamless, digital border that will improve security and biosecurity while reducing friction for businesses.
"Whilst responsibility for Border Control Posts is a devolved matter, we are working closely with the Scottish government on the requirements for goods arriving in Cairnryan."