Warrenpoint Harbor will need a 40,000-square-foot facility to conduct Brexit-related controls on UK goods, the region's MP said.
South Down MP Chris Hazzard said it would include truck parking and offices.
However, CEO of the port, David Holmes, said it is currently "unclear what requirements may be required for the construction of a new port infrastructure".
He added that government clarity is "now an absolute imperative".
Mr. Hazzard von Sinn Féin admitted that “there is still great confusion about what exactly is being proposed; Who pays the bill? and when construction will begin ”.
"The UK government urgently needs to put its cards on the table and bring some transparency to the process," he said.
At the end of the Brexit transition period in January, Northern Ireland will continue to follow EU rules on agricultural and industrial goods, while the rest of the UK will not.
In addition, all of Britain will leave the EU Customs Union, but Northern Ireland will continue to enforce the EU Customs Code in its ports.
This means some new controls and procedures for goods entering Northern Ireland and other parts of the UK.
The UK government said this would not require new customs infrastructure, but an expanded regulatory control infrastructure.
Last week, East Antrim MP, Sammy Wilson of DUP, said the port of Larne was planning to use up to 14 acres of land for parking and building trucks.
Executives from Northern Ireland's ports will testify before a Stormont committee on Wednesday.