Jonathan Jones becomes the sixth senior civil servant to leave the government this year amid growing tensions between the prime minister and Whitehall.
The Financial Times reported that Jones quit over Johnson’s plan to unilaterally claim powers for the UK to decide how sections of his own Brexit withdrawal agreement (WA) covering trade in Northern Ireland work.
Several experts believe the proposals in the Internal Market Bill, due to be published on Wednesday, effectively breach the WA that Johnson negotiated to take the UK out of the EU.
The plans risk collapsing crucial Brexit negotiations on a longer-term trade deal, ongoing in London now.
Jones’ departure came as the hardline Tory Brexiteer European Research Group (ERG) declared that “Brexit is not done” until Johnson succeeds in nullifying key parts of the WA.
If the talks break down the UK would default World Trade Organisation terms for trade with the EU from January, which is likely to cause at least short-term economic damage.
A spokesperson for the attorney general’s office confirmed Jones’ departure but would not comment on his motivation.
“We can confirm that Jonathan Jones has resigned. We won’t be commenting further,” they said.
The EU has made clear that any attempt to renege on the WA would risk a collapse in negotiations.
A Brussels spokesperson insisted on Monday that insisting that implementing the WA is a “precondition” for negotiations on a trade deal, declaring it a “matter of trust”.
Downing Street has stressed the moves are simply a “safety net” to ensure there is not legal confusion if the UK and EU, through the so-called “joint committee” that monitors the implementation of the WA, cannot agree on Northern Ireland.
A UK official has also insisted it is “completely committed” to the WA, and described the legislation as “minor clarifications”.
But experts told HuffPost UK the moves are at the very least a first step towards reneging on the WA.
Sir Bernard Jenkin, who chairs the steering group of the Tory Eurosceptics’ body ERG (European Resource Group), said: “If we don’t reach a deal with the EU, Brexit is not done until the UK government succeeds in its determination to assert its own interpretation of the withdrawal agreement.
“If the EU is unwilling to do a deal with us, there are two options. The first is to enact domestic legislation that will largely nullify the direct effect and direct applicability of EU law. We have the mandate and majority to do this.
“Second, if the EU insists on an unreasonable interpretation of the withdrawal agreement, the UK must stand ready to repudiate it.
“I hope it is not necessary, but if it is the only way to achieve UK prosperity and the kind of sovereign independence which is the democratic right of any nation recognised under the UN Charter, then so be it.
“And most other nations would respect us for that.”
Jones’ departure follows the exit of cabinet secretary Sir Mark Sedwill, Simon McDonald from the Foreign Office, Philip Rutnam from the Home Office amid a row with home secretary Priti Patel, Richard Heaton from the Ministry of Justice and Jonathan Slater from the Department for Education following the summer’s exams fiasco.