Boris Johnson has walked into a diplomatic row with one of the UK’s closest allies after claiming the prime minister of the Netherlands had been seeking to “mediate” between Brussels and London over the post-Brexit arrangements for Northern Ireland.

Speaking to reporters on a plane to New York for a meeting of the UN general assembly, the prime minister suggested the Dutch government was looking to act as a mediator between the European Commission and London on the differences that have arisen in recent months.

“I talked to Mark Rutte [the Dutch PM] the other night, who wanted to come and see if he could mediate on the issue and I said, you know, we really want to make progress,” Johnson had said. “We seek a solution, but it has to be one that allows the free movement of goods between all parts of our country.”

Dutch diplomatic sources expressed surprise at the prime minister’s comments, insisting that Rutte had instead specifically urged Johnson to be pragmatic in his dealings with the European Commission.

The EU’s executive branch has been tasked by member states with ensuring the UK implements the withdrawal agreement, including the Northern Ireland protocol setting out the post-Brexit border arrangements. Dutch sources rejected any suggestion that the commission was being sidelined through bilateral discussions or that there was a division among the 27 member states on the issue.

“The [Dutch] prime minister called on Boris Johnson to be constructive, pragmatic and engage with the commission,” a Dutch diplomatic source said of last week’s meeting between the two leaders. “Both the UK and EU share the responsibility to make the protocol as negotiated and ratified on both sides of the Channel work for the people in Northern Ireland.”

The latest spat comes at a difficult time for UK-EU relations with the European Commission and the union’s 27 member states.

The French government has in recent days expressed its fury over the UK’s involvement in the Aukus security partnership with Australia and the US, which has cost France a €90bn submarine contract. One French minister described Britain as being in “vassalage” to America.

Relations are, however, at risk of deteriorating further in the coming months. The prime minister has repeatedly warned that the UK will not hesitate to trigger article 16 – the override mechanism that would suspend parts of the Northern Ireland protocol, which is designed to avoid a hard border on the island of Ireland.

Johnson has demanded a renegotiation of the terms of the protocol, which effectively leaves Northern Ireland in the EU’s single market and establishes a customs border within the UK down the Irish sea.

The EU has refused any such negotiation but is expected to offer some solutions to other onerous checks and paperwork in the first two weeks of October. Lord Frost, the cabinet minister responsible for Brexit issues, has warned that changes in the margins will be insufficient.

Asked on the plane to New York whether he intended to trigger article 16, Johnson had suggested he wanted to find a pragmatic solution, but added that “the current situation can’t go on for ever”.

He said: “I don’t believe it’s sensible, 20% of all checks in the whole of the perimeter of the EU are now done in Northern Ireland. So we do need to sort it out, we need to sort it out fast.”