As the Prime Minister faced fresh questions over trade within the UK after Brexit, Arlene Foster said Government officials had told her there would need to be checks.
Asked on BBC Radio 4's Today programme about the sense of some in the unionist community that Mr Johnson's deal was a "betrayal", she said: "I think it is right for the leadership of unionism in Northern Ireland to try to work with the prime minister of the day to get the best deal for Northern Ireland.
"We will always do that. We will continue to do that. I think it says more about the person who broke their word than me and the leadership of the... Democratic Unionist Party."
She said the DUP had been told by HM Revenue and Customs (HMRC) officials before the PM announced his deal that there would be checks between the mainland and Northern Ireland.
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Mrs Foster said a lack of free-flowing trade would cause "economic instability in Northern Ireland, which will lead to higher costs for retailers which will lead to less choice for our consumers in Northern Ireland".
"And all of that leads me to say that we need to - after this election is over, and I'm not prejudging the election in any one way, every vote will count - but what is important is that we have a strong team of DUP MPs back in Westminster to speak up for Northern Ireland."
Mrs Foster has kept a low profile in the election campaign thus far, and her intervention will be seen by some as an attempt to highlight a need for the DUP's role in holding sway in the event of a hung parliament.
Her comments came after Labour released a leaked Treasury report last week that concluded customs checks and possibly even tariffs could be required on goods travelling in both directions between Northern Ireland and Great Britain.
But Mr Johnson told Sky News' Sophy Ridge On Sunday programme over the weekend that the report was "wrong" and added that the six counties would have "unfettered access" to the UK market.
With just a few days to go until polls open, the PM is embarking on a blitz of Labour's heartlands in a bid to convince Leave voters that Jeremy Corbyn's Brexit position is akin to a "great betrayal", and will say there are just "three days to get Brexit done".
He has consistently vowed to take the UK out of the EU by January 31 and then finalise a trade deal with Brussels within 11 months to meet the transition period deadline.
Arrangements would also need to be signed off that allow Northern Ireland to continue to follow Brussels and Dublin rules on the trade of goods to ensure there is no hard border.
But a Whitehall report seen by the Financial Times highlights the difficultly involved for the Government in bringing in the infrastructure in time for the UK to leave when the PM has pledged.
A Department for Exiting the European Union document, according to the FT, states that: "Delivery of the required infrastructure, associated systems, and staffing to implement the requirements of the (Northern Ireland) protocol by December 2020 represents a major strategic, political and operational challenge."
Elsewhere on the campaign trail, shadow chancellor John McDonnell set out Labour plans for a budget on February 5 which he said will save the NHS, rebuild public services, and introduce a Real Living Wage of £10 per hour for all workers over 16.
In the first 100 days of a Labour government, the process of bringing water and energy into public ownership will begin, with boards set up to run the utilities.
In a speech in London, Mr McDonnell said: "I can tell you today that my first act as a chancellor will be to write to the Office for Budget Responsibility and we'll ask them to begin their preparations for my first budget which will be given on February 5, the date when almost 10 years of cuts will come to an end."
Mr McDonnell also said he would "expect" the DUP to support a Labour government's programme.
"Over the years I have worked with individual DUP politicians. I can't see them voting against the Real Living Wage, I can't see them voting against the levels of investment that we want to put in right the way across the country, including Northern Ireland.
"I can't see them voting against the funding that we want to put into the NHS, education and our public services overall. So I would expect them to support a Labour government's programme as we implement it."