The Tánaiste Simon Coveney had said that if Boris Johnson's latest Brexit proposal is his final offer then there will be no deal.
However, Mr Coveney said he believes there are positives in the plan that can build towards an agreement.
Speaking in the Dáil today, he said the plans do not deal with the commitment for no border infrastructure on the island of Ireland.
He also stated that they would not facilitate the functioning of an all-Ireland economy which had been committed to in the withdrawal agreement with the backstop.
The Tánaiste said: "The customs proposal is a problem.
"If that is the final proposal, there will be no deal.
The major concerns over the plans are customs checks, including where and how they would be done.
Additionally, there are fears the Northern Ireland vote on keeping trade rules aligned to the EU or not would give the DUP an effective veto.
However, he said that while there are "fundamental problems" with the protocols, he hopes they can be "stepping stones" towards securing a deal.
DUP MP Jeffrey Donaldson said this morning that there will be no customs posts on the border under the terms of Boris Johnson's Brexit proposal.
Mr Donaldson said that the plan"is a reasonable attempt to reach a compromise" but that the EU was not willing to do so.
Meanwhile, the British Prime Minister has told MPs that his latest Brexit proposals are "a genuine attempt to bridge the chasm".
Mr Johnson said the UK government's objective "has always been to leave with a deal" and that his "constructive and reasonable proposals" indicate their "seriousness of purpose".
However, Labour leader Jeremy Corbyn said the proposals were "simply unworkable".