Brexit Secretary David Davis was answering questions in the House of Commons this morning to update Parliament on progress made.
Yesterday, the House of Lords defeated the Government for the tenth time on its key Brexit legislation with an amendment introduced by Lord Patten.
This called for no border checks in Northern Ireland - potentially forcing the UK to remain in the Customs Union.
Prime Minister Theresa May had already suffered a string of crushing setbacks, including backing for MPs to be able to vote down a "no deal" Brexit and remaining in the Customs Union.
The amendments risk undermining the Government's negotiations with the European Commission, and could even block Brexit if they were adhered to.
Speaking in the House of Commons this morning, Conservative MP for Maldon John Whittingdale asked: "Is this task not going to be made any easier and indeed considerably harder by some of the amendments passed on the EU Withdrawl Bill?
"Does he agree they will need to be repealed when they come back to this House and the Lords will press them at their peril?"
Responding, the Brexit Minister Davis warned some of the amendments could impact significantly on negotations.
He said: "This is an essential bill in the national interest.
"The upper house has a very important job in approving the content of the legislation but some of the proposals put forward by the House of Lords could have the effect of undermining the negotiations.
"That is of course a critical national interest and we will have to deal with that accordingly."
The Brexit Minister also warned that some of the amendments "would be a gift to negoiators on the other side".
He said: "Some of the proposals, for example, putting timetables into the negotiating arrangements, at which point control is taken away from the government, would be a gift to the negotiators on the other side."
Mr Davis added that "significant process" had been made in negotiation the UK's exit from the EU with the agreement of terms to a "time-limited implementation period and locking down entire chapters of the financial citizens and citizens' rights".
The cross-party amendment put forward by Lord Patten yesterday called for the Government to respect the Good Friday Agreement