But, in an interview on Sky News's Sophy Ridge On Sunday, Mr Johnson said the checks would not be on goods travelling into Britain from the six counties.
He said: "The deal we've done with the EU is a brilliant deal and it allows us to do all the things that Brexit was about so it's about taking back control of our borders, money, laws - but unlike the previous arrangements it allows the whole of the UK to come out of the EU including Northern Ireland."
Mr Johnson said the leaked Treasury analysis document that Labour revealed on Friday was "wrong" to suggest there could be checks and even tariffs on good travelling between the two parts of the UK.
He added: "There's no question of there being checks on goods going NI/GB or GB/NI because they are part of - if you look at what the deal is, we're part of the same customs territory and it's very clear that there should be unfettered access between Northern Ireland and the rest of GB."
Also on the programme, the Prime Minister refused to be drawn into whether he would resign if he fails to win a majority in Thursday's General Election.
He was asked three times by Sophy Ridge if he would stand down if he fails to secure a majority.
The Prime Minister admitted he was nervous and “fighting for every vote” ahead of the poll, but when asked if he would resign if it did not go his way, he replied: “The choice on Thursday is unbelievably stark, it’s between going forward with a one nation Conservative government that can get Brexit done…
“Or spending the whole of next year in complete paralysis with two referendums, one on Scotland, one on the EU when Jeremy Corbyn cannot even tell us what his position is on Brexit and who is going to campaign for the deal that he proposes to do.”
Pressed again, Mr Johnson said: “If you don’t mind, Sophy, what I’m going to do is concentrate on the five days before us because that is what I think the people of this country would expect.
“We have got a very short time to get our message across, it’s a message of hope and optimism about this country.”
Mr Johnson also guaranteed that immigration to the UK would fall under his proposed system after Britain has left the EU.
“I can make sure that numbers will come down because we’ll be able to control the system in that way and what I don’t think is right is to have an uncontrolled and unlimited approach to that,” he said.
Mr Johnson continued: "I don't think people in this country are hostile to immigration at all, let alone being hostile to immigrants, but they want it democratically controlled and that's what Brexit allows us to do."
The Prime Minister said that Jeremy Corbyn's policy of "complete free movement" is "absolutely not what people voted for".
He said: "You've seen quite a large number of people coming in from the whole of the EU, 580 million population, able to treat the UK as though it's basically part of their own country and the problem with that is there has been no control at all and I don't think that is democratically accountable.
"You have got to have a system by which politicians can say to people, well yes we are letting people in but we are doing it in a way that is controlled and checked."
But shadow health secretary Jonathan Ashworth said Boris Johnson is "misleading" the British people by saying he will bring immigration levels down.
Mr Ashworth told Sky's Sophy Ridge: "We should have a fair and balanced immigration system, of course we should, but he's (Boris Johnson) imposing a tax on nurses coming from the EU and beyond, to come and work for our NHS to care for our sick and elderly, he's going to exacerbate the staffing crisis in our NHS with his proposals.
"And he's also misleading the British people, because he's trying to give them the impression that he's going to be bringing immigration down, but when you look at the details of what he's announced today, he's saying he's going to hand over decisions on who will get a visa to an independent committee."
The Prime Minister confessed to having sometimes ridden a bicycle on the pavement when he was asked to reveal the naughtiest thing he has ever done.
“When I was riding a bicycle every day which I used to do, I may sometimes have not always obeyed the law about cycling on the pavement,” he admitted.
“I may sometimes, OK – but I want you to know how firmly and strongly I disapprove of people who cycle on the pavement and I think it’s wrong and I feel bad about it but I might sometimes have scooted up onto the pavement rather than dismounting before.”
The Labour leader held up classified documents during the campaign which detailed trade talks between the US and UK which he said were part of "secret talks" to sell off the NHS.
Mr Johnson described the reports as "nonsense" while Labour said the document proves that the Tories are willing to privatise parts of the NHS in order to secure a trade deal with the US.