Steve Baker said he had heard “extraordinary allegations” that Treasury officials have been deliberately seeking to promote staying in the customs union above other options.
It follows the leak of damaging government economic analysis showing that all available Brexit scenarios would damage the economy, which earlier this week prompted Mr Baker to suggest civil servants were “always wrong”.
The comments drew a grimace from the Brexit Secretary David Davis, who was sitting next to him on the government front bench.
Mr Rees-Mogg added: "If this is correct, does he share my view that it goes against the spirit of the Northcote rebellion reforms that underpin our independent civil service?"
Mr Baker responded that the account was "essentially correct", telling the Commons: "I think it would be quite extraordinary if it turned out that such a thing had happened."Mr Baker said: "At the time I considered it implausible because my direct experience is that civil servants are extraordinarily careful to uphold the impartiality of the civil service.
"I think we must proceed with great caution in this matter but I heard him raise this issue. I think we need to be very careful not to take this forward in an inappropriate way. But he has reminded me of something which I heard.
"I think it would be quite extraordinary if it turned out that such a thing had happened."
Mr Baker was challenged by opposition MPs as he delivered his answer, prompting him to reply: "I didn't say it was correct. I said the account that was put to me is correct.
"It was put to me, I considered it an extraordinary allegation, I still consider it an extraordinary allegation."
He added: "To be absolutely clear, I said it was correct that the allegation was put to me. I did not in any way seek to confirm the truth of it.
"But what I would say is we need to proceed with great caution because it is essential we continue to uphold and support the impartiality of the civil service."
Earlier, Mr Davis told MPs that he was aware of the leaked analysis last year and made clear to the Exiting the European Union Select Committee on December 6 that the government would "quantify the effect of different negotiating outcomes as we come up to them".
He told the Commons: "Actually, I told the select committee that this work was underway last December."
Responding to his Labour opposite number Keir Starmer, Mr Davis said: "One of the things [Mr Starmer] has been trying to pretend over the course of the last few days is that somehow my colleagues have been critical of the civil servants doing its job because the outcome is as yet a work in progress.
"That is what it is, a work in progress.
"I say that because we are trying to do something which is incredibly difficult."
He continued: "Every forecast that has been made about the period post-referendum has been wrong."