Belfast Harbour does not expect to introduce any immediate changes to its procedures as a result of Brexit.
However, officials said they were working to be prepared for what may come out of the future trade talks between the EU and UK.
The comments come after the boss of ferries operator Stena Line said his firm was preparing for new checks to be carried out at British ports.
Stena boss Ian Hampton told the BBC that there will be a border down the Irish Sea at the end of the transition phase of the Brexit process. That is currently December 31.
Belfast Harbour told the Belfast Telegraph that no immediate changes to its procedures are expected during the transition period.
A spokesman for Belfast Harbour said the port currently handles more than 70% of Northern Ireland's seaborne trade.
"A key priority for us is to ensure the smooth flow of goods and people through our port with minimum disruption," the spokesman said.
"As the UK formally exits the European Union and moves into a period of transition, Belfast Harbour continues to engage with government and its agencies, along with our customers and terminal operators, so that we are prepared and ready to deal with any operational implications of future trade agreements.
“We do not expect any immediate changes to our operating procedures during the transition period.”
Warrenpoint Port also said there was no new checks or inspections on trade coming into Northern Ireland from Great Britain.
"We are, however, continually working to maximise the flexibility of the harbour estate in order to ensure we can respond quickly to any future changes," it said in a statement.
Belfast International Airport said it has not introduced any changes to infrastructure during the transition period.
"We will work closely with government departments should there be any requirement for additional checks to be made on goods incoming from GB," a spokesman said.
We do not expect any immediate changes to our operating procedures during the transition period.Belfast Harbour
Stena Line operates a fleet of ferries connecting Great Britain to the island of Ireland and owns three ports on the routes. It wants to know the physical changes required on what has, until now, been frictionless trade.
"The complication in the Irish Sea is where they have moved the border. The border is now physically a sea border rather than a land border," Mr Hampton said.
When asked whether there will be checks on trade between Great Britain and Northern Ireland, he said: "Yes, that is as it sits.
"But let's be future focused. These only come in after the transition period so the January 31 date is just a date. Formally when we leave, we leave the EU but with the transition period there is no change.
"If we do not progress, if we do not use this time wisely, then of course we could encourage a rethink. Let's not have a date where we fall of the cliff slightly later in the year. So we have the 11 months.
"I think government has learnt an awful lot by partnering with business and I would encourage that."
Mr Hampton said that the final quarter of the year will be vital for businesses and called on the British Government to clarify what changes it will pay for if checks are introduced.
"If we know by then that we don't have a trade deal, then we will have to default to maximum checks as a hypothesis, then temporary infrastructure can be brought in to play," Mr Hampton said.
"You need to have the space to do the necessary checks. You need to be able to house necessary officials from governments to be able to carry out and perform their role to protect the border- which is important- it is an obligation of being a port owner to the state."
The UK formally left the EU on Friday January 31 but will continue to follow EU regulations on trade until December 31 2020, unless the transition period is extended.
Trade talks between the EU and the UK are set to begin in March, with a view to having a new trading relationship established by the cut off point in December.