Rehman Chishti, the Prime Minister's Special Envoy for Freedom of Religion or Belief (FoRB), has resigned over Boris Johnson's plans to override the Brexit deal and ignore international law.
In his letter of resignation, Mr Chishti said he was "committed to delivering Brexit" but could not support the Internal Market Bill in its current form.
"I have real concerns with the UK unilaterally breaking its legal commitments under the Withdrawal Agreement," he wrote.
"During my 10 years in Parliament and before that as a Barrister, I have always acted in a manner which respects the rule of law.
"I feel strongly about keeping the commitments we make; if we give our word, then we must honour it.
"Voting for this Bill as it currently stands would be contrary to the values I hold dearest."
The Special Envoy for Freedom of Religion or Belief (FoRB) was a position created by former Prime Minister Theresa May to "promote inter-faith respect and dialogue internationally".
Mr Chishti was only the second incumbent of the post after Lord Ahmad of Wimbledon.
The Prime Minister's Brexit plans have been widely condemned by MPs and former prime ministers, including David Cameron, who told reporters on Monday that "passing an act of parliament and then going on to break an international treaty obligation is the very, very last thing you should contemplate".
"It should be an absolute final resort, so I do have misgivings about what is being proposed," he said.