Mr Percy last night voted against the Government, along with Sir Roger Gale, with 30 abstaining or otherwise not voting.
But the UK Internal Market Bill cleared its first Commons hurdle yesterday despite deep misgivings by some senior Tories.
Mr Johnson’s controversial plan passed its second reading by 340 to 263 – a Government majority of 77.
But Tories have continued to rally against the plans, which will be analysed in greater detail today when MPs go through detailed line-by-line scrutiny of the Bill.
Government whips are bracing themselves for expected votes next week on amendments to the Northern Ireland provisions which some rebels may back.
A number of Conservative former ministers have made clear they would not support any measure that breached international law, including former chancellor Sajid Javid, Andrew Mitchell and two former attorney generals, Geoffrey Cox and Jeremy Wright.
But Mr Percy indicated to website Politico that he would not back an amendment tabled by Sir Bob Neill, chairman of the Commons Justice Committee, requiring a vote of Parliament before ministers can exercise the new powers in the Bill.
Mr Percy said: “I’m mainly concerned with the way the Government has presented this issue, rather than the principle itself which may be necessary in extremis. However, it has been presented appallingly and no mention has really been made of the EU’s unreasonable behavior.”
Former Northern Ireland Secretary and Skipton and Ripon MP Julian Smith abstained from the vote, while other Yorkshire Tories backed the Government.
Wakefield’s Imran Ahmad Khan said during the debate: “Although I stand four-square behind the Government’s policies and objectives, including those advanced by the Bill, I cannot vote for legislation that a Cabinet Minister stated from the Dispatch Box will break international law.”
But he later said: "Having consulted highly respected experts in international law, some of us have concluded that if the EU, in breach of its obligations to act in good faith and with best endeavours, were to employ the withdrawal agreement as a Trojan horse, this Bill, if enacted and employed, would not necessarily constitute a breach of our commitments, under either UK or international law. Rather, the Bill would then serve as a protection against the abuse of our good nature and a reminder to the Commission of its obligations."
He said his "great problem with the Government’s position is the predicament in which they have placed people who share my view" by Northern Ireland Secretary Brandon Lewis saying that it would break international law in a “specific and limited” way.
He said: "I simply reject the notion that we would be in breach of our international obligations."
Mr Ahmad Khan then received assurances from that his interpretation, that employing the powers of the Bill would not break international obligations, was a shared interpretation by the Government.
He said afterwards: "In my speech, I underscored that my reservations with the UK Internal Market Bill were founded on a Cabinet Minister stating at the Dispatch Box that it would ‘break international law’. My concluding comments in the speech clearly stated that only if my right hon. Friend the Chancellor of the Duchy of Lancaster, in his response to the debate, can provide assurances to the House that Her Majesty’s Government share my interpretation—our interpretation—that such powers, if enacted and employed, would not automatically constitute a breach of our legal obligations will I support the Bill.
"Following my speech, I met with the Chancellor of the Duchy of Lancaster, the Prime Minister and the Attorney General - all of whom assured me that Her Majesty’s Government shared my interpretation that employing the powers of this Bill would not break our international obligations or indeed international law. I was therefore able to vote in favour of this Bill in good conscience."