Work on the customs centre is already well underway in a bid to have it ready in time to carry out new post-Brexit checks that will be required from the start of next year.
A report published ahead of the Wednesday meeting says the 'economic significance' of having this in place outweighed 'limitations' with its design.
'Although the proposal presents design limitations and does not create a complete picture of sustainability by failing to demonstrate how it complies with all relevant national and local planning policies, these disappointing aspects of are still considered to be outweighed by the economic significance and statutory necessity for the port to have new infrastructure in place by January 1,' it says.
Just off the M275, the border control point will be used to carry out checks of all plant and animal products, including live animals, entering the country through the port.
Savills, the port's planning agent, had urged the council to 'swiftly' consider the application following its submission last month in order to allow the facility to be in place ahead of the introduction of the new requirements.
Earlier this month, the council's cabinet approved the decision to award the contract to run the centre to Portico Shipping.