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MPs were planning to spend up to six hours on Wednesday finishing the Bill’s committee stage, which involves line-by-line scrutiny.
But Mr Bone said time will be added on to allow the Bill to receive a third reading, clearing the way for it to be sent to the House of Lords.
Peers are expected to contest parts of the Bill when they consider it after the summer recess, setting up a lengthy showdown between the two Houses.
Mr Johnson’s Government has said the measures to remove checks on goods and animal and plant products travelling from Great Britain to Northern Ireland are necessary to safeguard the Good Friday Agreement and peace and stability.
But the plans have been widely criticised by the EU while Tory former prime minister Theresa May has questioned the legality of the Bill.
Mr Bone, raising a point of order following the conclusion of the Bill’s second day of committee stage, told MPs: “Given the progress of the committee of the whole House we will now take the Third Reading of the Northern Ireland Protocol Bill tomorrow.
“A supplementary programme motion will be tabled tonight to provide for an extra hour of debate tomorrow.”
Outgoing Prime Minister Mr Johnson has denied his departure from Downing Street will be the end of Brexit, claiming some people believe Labour and the “deep state will prevail in its plot to haul us back into alignment with the EU as a prelude to our eventual return”.
The Bill’s second day of committee stage in the Commons saw Alliance MP Stephen Farry warning that “chaos” would be created in many sectors of the Northern Ireland economy if the new “dual regulatory” is introduced.
The North Down MP put down an amendment, which would have imposed conditions before the option to choose between dual routes could be implemented, but it was rejected by 293 votes to 201, majority 92.
Cabinet Office minister Michael Ellis said: “If a Northern Ireland-based business trades north-south on the island of Ireland then they can continue, as now, to follow EU rules and sell their products in the EU and across the UK because of the Government’s commitment to unfettered access.
“But if their business model is UK focused they can choose to follow UK rules and benefit from the opportunities afforded there.”
Mr Ellis also told MPs: “No business will be worse off as a result of UK action.
“The Bill before this House forces no change on any sector, but allows ministers to respond to any specific asks from each sector, if appropriate. And I have heard strong views of what sectors of the Northern Ireland economy think, particularly dairy as I say, and this is why understanding such concerns is at the heart of our work.
“And why we are engaging with stakeholders and have been doing so and will continue to do so.”
Earlier, Mr Farry said: “If this dual regulation was implemented, it would bring major consequences, it would create chaos in many sectors of the Northern Ireland economy, and we would increase risk of economic crime, including smuggling.
“Even the Bill itself entails uncertainty for investment decisions, never mind the implications when it comes to full application.
“It would mean that North Ireland would lose access to the single market for goods, both in practice, as companies in the Republic of Ireland or the rest of Europe (would) see Northern Ireland products as risky and also as a matter of law.”
The DUP did not support any amendments to the Bill, with the party’s leader and Lagan Valley MP Sir Jeffrey Donaldson saying: “We do not believe they are necessary in order to achieve the objectives that are required.”
MPs also voted voted 293 to 205, majority 88, to defeat the amendment put forward by Labour, which would have required an economic impact assessment to be carried out before a minister could make any provisions for the dual regulatory regime.