Her minority government could easily be defeated on the customs issue if pro-Brussels Tories back the Labour Party and other anti-Brexit MPs, as well as on 14 other amendments to the EU Withdrawal Bill from Peers.
Housing minister Dominic Raab said he was "reasonably confident" the government, which will have the support of a handful of pro-Brexit Labour MPs and the 10 Democratic Unionist MPs, would prevail.
The "meaningful vote" will be the first major test after the House of Lords introduced 15 changes to the bill, trying to reshape the government's approach to Brexit by encouraging lawmakers to press for the closest possible ties.
However, anti-Brexit Tory MP Dr. Phillip Lee was unconvinced, resigning from his government job as a Justice Minister and publicly attacking the Prime Minister at the 1922 meeting.
MPs are preparing for a two-day debate on the legislation to leave the EU.
The government says that would undermine its negotiating position in talks to leave the bloc and Brexit minister David Davis warned lawmakers the government would never allow them to reverse Brexit.
'But the message we send to the country through our votes this week is important.
Another would give Parliament the power to approve or deny the Brexit withdrawal agreement and transitional measures, preferably before the European Parliament debates and votes on it.
Speaking to reporters outside the meeting, Solicitor General Robert Buckland confirmed the Government was in discussions with rebels about establishing a fresh amendment committing to seek a customs arrangement - not a union - with the EU.
"We are asking members of parliament to abide by the referendum result, our manifesto commitment and to back our country", Andrew Bridgen, Conservative lawmaker and Brexit campaigner, told Reuters.
"The main reason for my taking this decision now is the Brexit process and the government's wish to limit parliament's role in contributing to the final outcome in a vote that takes place today", Lee, who voted to remain in the European Union during Britain's 2016 referendum, said on his website. MPs will vote on this particular amendment this afternoon.