Margaritis Schinas made the comments at the Commission’s daily media briefing.
If he was pushed to speculate what might happen in a no-deal scenario, he said it was “pretty obvious you will have a hard border”.
However, last week the British Prime Minister said the EU had made it “clear there will be no flexibility on border checks in no deal”.
“The Irish government will be expected to apply EU checks in full,” added Theresa May.
Mr Schinas told reporters at Tuesday’s briefing: “If you’d like to me to push me and speculate on what might happen in a no-deal scenario in Ireland, I think it’s pretty obvious – you will have a hard border.
“And our commitment to the Good Friday Agreement and everything that we have been doing for years with our tools, instruments and programmes will have to take, inevitably, into account this fact.
“So, of course we are for peace; of course we stand behind the Good Friday Agreement but that’s what a withdrawal… that’s a no-deal scenario, that’s what it [would] entail.
“So I will not now speculate on this Plan B because as I said seconds ago we are for Plan A which is set by the Withdrawal Agreement and the Political Declaration as a package.”
Drivers in Derry have already been warned of the consequences of a hard border with Donegal.
If they drive into Donegal in the event of a no-deal Brexit, they will have to have a special ‘green card’ from their insurance company to prove they are insured to drive in the Republic which is in the EU.