On Tuesday, legislators in the House of Commons handed the government a symbolic defeat by backing an amendment to the Finance Bill that puts roadblocks in the way of government spending on "no-deal" preparations.
British legislators have slashed the time Prime Minister Theresa May's government will have to formulate a plan B if her widely criticised Brexit deal is rejected in a crucial parliamentary vote next week.
"My understanding is the motion is amendable, I'm clear in my mind about that", Bercow said.
But Mr Bercow defended his decision amid jeers and heckles from the Tory benches, saying: "I'm trying to do the right thing and make the right judgments".
"That is what I have tried to do and what I will go on doing".
Barry Gardiner, the opposition Labour Party's shadow global trade secretary, said earlier his party will table a no confidence motion in the government if - as expected - Parliament votes down Prime Minister Theresa May's Brexit deal.
Ian Murray, a Labour MP who supports People's Vote, a group campaigning for a second referendum, said Parliament has "now asserted its authority and sovereignty and effectively exposed the threat of no deal as an empty one".
"Isn't the prime minister bringing back exactly the same deal she admitted would be defeated four weeks ago?" he asked.
May has refused to retreat from her unpopular deal, which envisages close trading ties with the European Union after leaving in March.
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"The real question for Members of Parliament who voted to give the public a say through the European referendum in 2016, who voted in large numbers to trigger Article 50, is the effect of triggering Article 50 is you either have a deal and the EU have been clear that the only deal on the table is the PM's deal".
"There is a question of extension of Article 50 and that may well be inevitable now given the position that we are in, but of course we can only seek it because the other 27 (member states) have to agree", he said.
The No 10 source said the Prime Minister had always meant to "respond quickly" if she fails to secure the support of the Commons.
Some Brexit supporters say a no-deal exit is the only way to truly leave the bloc and that warnings of the economic consequences have been overblown to drum up support for May's plan. I genuinely think we can't do it on March 29 this year.
Opposition to May's deal is spread across the political spectrum, including sections of her own ruling Conservative Party and the 10 Northern Irish Democratic Unionist Party (DUP) MPs her government relies on to command a majority in parliament.
70% of Tory MPs believe that the UK would be able to quickly strike trade deals with the likes of the United States and China, and 58% of them are confident that such new trade deals would more than compensate for any lost European Union trade.
Mr Bercow said he had consulted privately with the clerk and other officials, but did not confirm his decision was taken with agreement from Sir David.
A top European parliamentarian urged British lawmakers to show "responsibility" over the divorce deal.