Tariffs will also have to be paid on goods going from Great Britain to Northern Ireland that are "at risk" of being transported to the Republic.
Speaking on Thursday night, however, Boris Johnson stated there would be no tariffs or checks between Great Britain and Northern Ireland.
"When you come out of the EU customs union, which is what we [will] have done, you have to have some way of checking goods that might attract a tariff coming from the United Kingdom into Ireland are actually paid, if there is to be a tariff," he said.
"There will not be tariffs or checks on goods coming from GB to NI that are not going on to Ireland, that's the whole point.
"The great thing that has been misunderstood about this is that there will not be checks, and I speak as the Prime Minister of the United Kingdom and as a passionate unionist, there will not be checks on goods going from Northern Ireland to Great Britain.
"We are the government of the United Kingdom and we will not institute, or implement, or enact such checks."
Mr Johnson added that Northern Ireland has a "great deal" under his plans and will have "unfettered access" to Great Britain.
Many were quick to take to social media to point out the inconsistencies between what Mr Johnson said and what is stated in his negotiated deal.
Aodhan Connolly, director of the Northern Ireland Retail Consortium, tweeted: "The PM says 'there will not be checks or tariffs on goods coming GB to NI unless they are going to Ireland'. Do you want to tell him or should I tell him that this is NOT what it says in the deal?"
Liberal Democrat MP and Brexit spokesperson Tom Brake said: "Are you planning on contradicting every government document on Brexit, or just the more problematic pieces? As we're early in the campaign it would be good to know. Checks will be required in both directions."
Jonathan Portes, professor of economics at London's King College, said the PM's comments show he does not understand his own Brexit deal.
Brexit Secretary Stephen Barclay also previously told MPs that, under Johnson's deal, some checks would be required for goods travelling between Northern Ireland and Great Britain.
He said "minimal targeted interventions" would be needed for such goods, as Northern Ireland would remain aligned with Dublin and Brussels trade rules.
The PM was also criticised for praising the fact that his deal would give Northern Ireland "access to the single market" - despite wanting the opposite for the rest of the UK.
“Northern Ireland has got a great deal. You keep free movement, you keep access to the single market but you also have, as it says in the deal, unfettered access to GB," he said.
Tom Brake said: "The single market and freedom of movement are a great deal - even Boris Johnson recognises this.
“So why isn’t he keeping them for the whole of the UK as part of the many benefits of EU membership?"