The government has accused lawyers refusing to prosecute climate protesters or act for fossil fuel interests of "undermining" the rule of law and independence of the legal profession.
The solicitor general Michael Tomlinson said the pledge, made by over 100 lawyers, was "fundamentally at odds with the idea that every person is entitled to a fair trial".
But he was accused of making a "bad faith" argument and ignoring the ethical dilemmas lawyers face.
Six KCs are among more than 120 lawyers to sign a "declaration of conscience" last month stating that they will not prosecute peaceful climate protesters or act for companies pursuing fossil fuel projects.
The move puts them at odds with the Conservative government, which has made cracking down on climate protesters like Just Stop Oil and Extinction Rebellion a political priority. Ministers have criminalised a wide range of peaceful protest activities with their latest anti-protest legislation.
Barristers who signed the pledge have self-referred themselves to the Bar Standards Board for breaking the profession's "cab rank rule" which specifies that they must take cases they are qualified for if they are available.
The government did not comment on the pledge at the time, but in a written parliamentary answer Mr Tomlinson, the second most senior minister for legal affairs, blasted the move.
"The 'cab rank rule' is an important principle which safeguards the rule of law and ensures fair access to justice," he wrote.
"Action such as this undermines the independence of the legal profession and is fundamentally at odds with the idea that every person is entitled to a fair trial."
The Conservative MP said the impact of the action on the Crown Prosecution Service would be "negligible" and that there was "a large pool of high-quality advocates" who could step in.
"I am confident that these cases will be prosecuted without undue delay," he added.
The government has itself been accused of undermining the rule of law on issues ranging from Brexit talks to the prorogation of parliament.
Jo Maugham KC, one of the top barristers to sign the climate pledge, described the solicitor general's argument as "pretty feeble", adding that "it doesn't grapple with any of the nuance".
"I don't really see it as being anything like a kind of good faith attempt to wrestle with the competing ethical dilemmas," he told The Independent.
"The notion that the cab rank rule is necessary to the functioning of a legal system is just bonkers. Nowhere else in the world as far as I'm aware is there a cab rank rule. Their legal systems function.
"Even in the UK the cab-rank rule does not apply to the vast majority of the legal profession, so solicitors are not bound by it. Even at the bar the cab rank rule has profound exceptions."
Mr Maugham, who is director of the campaign organisation the Good Law Project, said many barristers circumvented the cab rank rule in practice by hiking their fees to avoid cases they did not want to take.
He added: "For some people it's really important and it does express a really important idea about access to justice, and I admire those people who adhere to it. But the reality is most people don't, and the legal system doesn't collapse. There's a touch of bad faith about it all I think."
The KC said some laws were “just not right” and that most lawyers would accept in principle that it would be wrong to enforce laws relating slavery, or in 1930s Germany.
The declaration says climate breakdown represents “a serious risk to the rule of law” and cals on legal professionals “to act urgently to do whatever they can to address the causes and consequences of the climate and ecological crises and to advance a just transition”.
The Bar Council of England and Wales says the cab rank rule prevents discrimination and described the action as "disappointing". The Criminal Bar Association said the pledge may have been "well-intentioned" but also "ill-thought out", adding: "Lawyers and commentators from across the political spectrum need to step away from bashing the criminal justice system into a political football."
