It now faces further scrutiny in the House of Commons, and also needs to be passed by the House of Lords.
PM Boris Johnson was forced to agree to table an amendment to his Internal Market Bill, giving MPs a vote on whether to use powers which would breach the deal brokered with the European Union previous year.
"Members of Johnson's government have previously admitted that the legislation, if passed, would 'break worldwide law in a very specific and limited way.' This set off alarm bells among lawmakers in Johnson's own party, many of whom said publicly that they would rebel and vote for measures aimed at pulling teeth from the bill next Tuesday".
However, the prime minister's intention to break global law riled dozens of Conservative MPs, leading him to agree to a compromise in which he must secure parliamentary approval before enacting his plan for Northern Ireland.
"In these circumstances I consider that it is my duty to tender my resignation from your government", Lord Keen added.
In a tweet on Thursday, he wrote: "At least Parliament will now have the chance to vote again if the government proposes to change the withdrawal agreement".
"The latest fudge by way of amendments doesn't take the problem away, it just changes the problem", he told reporters in Scotland.
He says the United Kingdom has to have the ability to break parts of the 2020 Brexit treaty he signed to uphold London's commitments under the 1998 peace deal which ended three decades of sectarian violence in Northern Ireland between pro-British Protestant unionists and Irish Catholic nationalists.
But Johnson, while telling a committee of senior MPs on Wednesday that he no longer believes the bloc is negotiating "in good faith", also said he hopes a free-trade deal will eventually be found.
Informal talks on a trade agreement are continuing in Brussels this week, ahead of another full-scale negotiation round later this month. There is fear in the US, EU, and in Westminster that a failure to uphold the Northern Ireland protocol, created to avoid a hard border on the island of Ireland, would lead to the return of physical border infrastructure between Northern Ireland and the Republic of Ireland.
European Commission chief spokesman Eric Mamer said: "We have as you know set out a position extremely clearly, it is in our statement and it relates to those clauses being withdrawn from the law. They've lost trust and undermined co-operation at the moment we most need it - and all to tear up an agreement they negotiated", Shadow Foreign Secretary Lisa Nandy said.
What is the Internal Market Bill?
Ursula von der Leyen, in comments made to reporters yesterday, said Downing Street's controversial UK Internal Market Bill had "distracted very strongly" from the two sides being able to secure fresh trade terms before the looming deadline.
Powers to override previously agreed obligations on state aid - government support for businesses.
He added that any agreed trade deal must prevent the return of a hard border on the island of Ireland.