The Tánaiste has admitted avoiding a hard border would be more complicated in the event that the Brexit deal, agreed by EU leaders, is rejected in the UK.
The European Council rubber stamped the deal yesterday after more than a year of negotiations between the EU and UK.
European leaders, including Taoiseach Leo Varadkar, suggested that it was the best possible deal the UK could expect.
European Commission President Jean-Claude Juncker said: "I say to the House of Commons this is the only deal possible.
"Those who think if they reject the deal they will get a better deal will be disappointed within seconds."
However, Theresa May now faces an uphill battle in getting MPs to sign off on the deal.
The agreement is facing opposition from not only the Labour party, but also a significant cohort of her own Conservative party.
The DUP - the Northern Irish party propping up Mrs May's government - has also warned it could withdraw support over the deal, which the party has vocally opposed.
Ahead of a House of Commons vote next month, Mrs May is again expected to address MPs today in a bid to convince enough of them to support the withdrawal agreement.
Simon Coveney says the UK rejecting the deal would be an outcome that would create challenges in a number of areas.
He said: "The consequences - in lots of areas, not just in terms of the challenge to prevent border infrastructure - in the absence of this deal passing is going to be much more complicated and far less attractive, I can assure you that.
"This is a stark choice - either the deal that's on the table, or something that's very uncertain that could have consequences we haven't planned for yet."
He added that he still believes a no deal Brexit is unlikely - but stressed that Ireland still has to prepare for the possibility.