Dominic Raab insisted that the United Kingdom is not prepared to "sacrifice" Northern Ireland amid suggestions from critics that Brexit could lead to a united Ireland.
Raab called the EU proposal for such an agreement "unacceptable" and said it ran the risk of condemning the United Kingdom to an "undefined limbo" within the customs union.
While progress has been made at the negotiating table on issues such as Gibraltar and the Sovereign Base Areas in Cyprus, Raab said Northern Ireland remains unresolved.
Writing in the Sunday Telegraph, he said: "According to our approach, the United Kingdom as a whole could remain in a customs agreement with the EU throughout the United Kingdom, but only for a brief period.
"The EU insists that it must be open, both EU proposals are unacceptable.
"The first threatens our precious Union, the second runs the risk of an undefined limbo within the customs union of the EU."
Raab said the "endorsement", which is effectively an insurance policy for all six counties across the Irish Sea, has not yet been agreed with EU leaders.
In the case of a Brexit without an agreement, this would mean that Northern Ireland would remain indefinitely in EU regulatory and customs agreements, to avoid a hard border with the Republic.
Raab, who was named secretary of Brexit in July after David Davis resigned in a dispute with the prime minister over his deal with Checkers, backed Theresa May's refusal to extend the implementation period as an alternative to support.
He said: "The United Kingdom has adopted a flexible approach, but we have always been clear and we can not leave Northern Ireland in a separate customs agreement.
"A line would collapse through the Irish Sea, threatening the economic integrity of the United Kingdom.
"That is something we will not tolerate. Nor can we see any difference in the regulation of Northern Ireland that threatens the domestic market of the United Kingdom. "
Deputy Esher and Walton in Surrey said that the EU proposals to "divide" the economic regime that unites the countries of the United Kingdom are "doubly irresponsible" because of the separatist movements that are emerging in Europe and because they would not serve the united front of the EU.
He insisted that while politicians are working to reach a good agreement with the EU leaders, the British public should be sure that deep down they are interested in all the countries of the United Kingdom.
Mr. Raab said: "We have extended the arm of friendship, but nobody should have doubts about our resolve to leave, or our willingness to defend the Union."
His comments come when Brexit's stalemate in the Irish border problem continues with Theresa May under pressure to make a breakthrough this week.