Writing in Saturday's Daily Telegraph newspaper, Johnson said the EU's stance justified his government's introduction of new legislation to rewrite its Brexit withdrawal treaty – a bill that is causing deep alarm among his own MPs, AFP reported.
Talks between London and Brussels on a future trading relationship are deadlocked as both sides struggle to prize apart nearly 50 years of economic integration, after British voters opted for a divorce.
Absent a deal by the end of this year, when the full force of Brexit kicks in, Johnson said the EU was bent on an "extreme interpretation" of rules for Northern Ireland.
"We are being told that the EU will not only impose tariffs on goods moving from Great Britain to Northern Ireland, but that they might actually stop the transport of food products from GB to NI," he wrote.
"I have to say that we never seriously believed that the EU would be willing to use a treaty, negotiated in good faith, to blockade one part of the UK, to cut it off, or that they would actually threaten to destroy the economic and territorial integrity of the UK."
The EU has threatened Britain with legal action unless it withdraws the contentious legislation by the end of September, and leaders in the European Parliament on Friday threatened to veto any trade pact if London violates its promises.
Johnson's accusation drew scorn from Luis Garicano, a Spanish member of the European Parliament.
"I think it's pretty ridiculous. I think Mr. Johnson insists on having his cake and eating it," he told BBC Radio on Saturday, noting that the treaty's protocol on Northern Ireland was plain to see when the prime minister signed it in January.
The government's claim that the treaty contains unforeseen problems was also undercut by a Financial Times report Saturday that British civil servants explicitly highlighted the potential issues in January, at least a week before Johnson signed it.
Under the EU withdrawal treaty, Northern Ireland will enjoy a special status to ensure no return of a border with EU member Ireland, in line with a 1998 peace pact that ended three decades of bloodshed.
The food dispute centers on the EU's refusal so far to grant Britain "third country" status, which acknowledges that nations meet basic requirements to export their foodstuffs to Europe.
The EU is worried that post-Brexit Britain could undermine its own food standards, as well as rules on state aid for companies, and infiltrate its single market via Northern Ireland.
After another difficult round of trade talks this week in London, chief EU negotiator Michel Barnier said "many uncertainties" remained about Britain's food export regime after January 1.
"More clarity is needed for the EU to do the assessment for the third-country listing of the UK," he said in a statement, ahead of another round of talks next week in Brussels.
Johnson said his government remained committed to finding agreement with the EU by the end of the year.
"But we cannot leave the theoretical power to carve up our country – to divide it – in the hands of an international organization," he wrote, calling the new UK Internal Market Bill a "legal safety net".
The prime minister's article appeared after he held a chaotic videoconference on Friday evening with mutinous Conservative MPs who are aghast at the prospect of the government tearing up an international treaty.
Senior Conservative backbencher Robert Neill was unimpressed by Johnson's calls to push the bill through and prevent a renewal of the Brexit infighting that paralyzed Parliament last year.
"I believe it is potentially a harmful act for this country, it would damage our reputation and I think it will make it harder to strike trade deals going forward," Neill told Channel 4 News.
The government crowed at one breakthrough Friday in clinching its first post-Brexit trade pact, with Japan. But critics noted it would boost Britain's long-term economic output by just 0.07 percent, and that trade with the EU is far higher.