Mr Johnson said he supported “passionately” the indignation DUP leader Sir Jeffrey Donaldson felt over the Protocol.
“Frankly the EU is implementing this in an insane and pettifogging way and we need to sort it out,” he said.
The UK accuses the protocol of having a chilling effect on British trade to Northern Ireland because of checks in the Irish Sea border to ensure goods meet EU standards.
Mr Johnson said he “never thought when we negotiated” the Protocol that there would be so many checks, which prevent the need for a hard land border with EU member Ireland.
He claimed that 200 businesses had stopped supplying Northern Ireland and some British food exports had been blocked.
Unionists fear the treaty is driving a wedge between the province and the rest of the UK.
The DUP claims that the Protocol is damaging the Northern Irish economy, which is contested by many who argue it will draw foreign investment to the country because it grants it access to both the UK and EU markets.
DUP falls behind Sinn Féin in polls
Sinn Féin has opened up an eight per cent lead over the DUP ahead of May’s Stormont election, according to a LucidTalk opinion poll for the Belfast Telegraph.
Sir Jeffrey, who has repeatedly threatened to collapse the assembly unless progress is made in Protocol talks, was the most unpopular Northern Irish political leader in the poll. Some 70 per cent of voters think he is doing a bad or awful job, including 54 per cent of Unionists
The UK and EU are negotiating to cut the number of checks on British goods meant solely for Northern Ireland. The UK and EU hope to cut a deal before the election to prevent it becoming a referendum on the Protocol.
Ms Truss and Maros Sefcovic, the European Commission vice president, met in Brussels on Monday to discuss progress in the negotiations.