Announcing a range of business supports for Irish businesses, Mr Martin said the Government is aware of the risks to vulnerable sectors.
“The Government will ensure it has done its own preparations in the ports and airports,” Mr Martin added.
“Even with a (trade) agreement there will be substantial challenges for supply chains and trade flows and checks.
“The protocol in Northern Ireland will apply.
“It is important that meaningful negotiations can only proceed on the basis of mutual trust.”
Minister for Foreign Affairs Simon Coveney said that Brexit is for real this time for traders and businesses.
National effort
“This time there is no extra time, there is no transition,” he said.
“We need a big national effort in the final three months to ensure no one is left behind. The key words are to, from and through.
“If you move things to the UK, if you buy from the UK and if you move things through the UK the status quo will not apply from January 1.
“We will continue to do everything we can to support Michel Barnier in his efforts to get everything in place in time.
“It must be consistent with the agreement already made.”
Mr Coveney added: “I would caution anyone who is thinking about playing politics with Northern Ireland on Brexit.
“Northern Ireland is too fragile and too important to be used as a pawn in the broader Brexit negotiations.”
Micheál Martin said that trust is “fundamental” in the conduct of negotiations.
He said he is to speak to the British Prime Minister Boris Johnson later today to raise the Irish Government’s “strong concerns” about comments made in the House of Commons on Tuesday.
Tánaiste Leo Varadkar has said that the Irish Government is appealing to businesses to take action and prepare for Brexit.
Brexit has not gone away and the next stage is happening.
“You need to be prepared for the new normal and you need to be ready now,” Mr Varadkar added.
“We are making available a grant of 9,000 euros per employee hired to enable businesses to build their capacity and manage any custom changes.
“My message to business people is simple – I know you are under a lot of pressure, I know you are being pulled in many directions and you’ve had a tough year, but Brexit has not gone away and the next stage is happening.”