The home secretary said the claims were "wrong" and a "surprise".
"I’m very surprised at Jacob, because he is famously courteous, famously thoughtful, articulate. So I’m very surprised that he’s used that language. I think that they are wrong, he is wrong here, and this document that he’s particularly referring to is not a Treasury document anyway," she said, speaking on the BBC's Andrew Marr show.
Forecasts about the impact of Brexit were leaked last week, indicating that the economy would grow at a slower rate after Britain leaves the EU. Rees-Mogg, a vocal Brexit supporter and backbencher, accused civil servants of trying to undermine the Brexit process.
Referring to the economic modelling, Rudd said: "It’s prepared across different departments and it’s a tool, it’s a tool for informing those of us who are on the EU subcommittee about the choices that are going to be made. It’s not about projecting one way or another. So I think they’re wrong.
"The UK government has to have forecasts in order to make certain decisions. Sometimes they’re wrong, but sometimes they’re wrong by degree, they’re still right about the direction it’s taking."
She added: "We have to approach them with a certain amount of cynicism but they help inform the debate and the decisions we make."
The former head of the civil service Gus O'Donnell also hit back at Rees-Mogg's claims.
"...if you’re selling snake oil you don’t like the idea of experts and testing your product and I think that’s what we’ve got, this backlash against evidence and experts is because they know where the experts will go," he said, speaking in ITV's Peston on Sunday.
Rudd meanwhile also reiterated the government's desire for a bespoke trade deal in which there is "frictionless" trade, no "Irish border gate" and that the UK can agree its own deals outside of the EU.
The Prime Minister Theresa May will this week convene a meeting of her top ministers to thrash out the Brexit negotiations in more detail amid the deepening split in her party about Brexit.
Rudd insisted that it would still have a "battle" with the EU over a bespoke deal that gives the UK its three demands.
"Frictionless" trade with the EU is widely seen as only possible if there is a customs union, something that would rule out deals with other countries, But, without such an agreement with the EU, there would be an issue over the Irish border.
"We know they’re [problems] there. That’s why we’ve said that we want to have a bespoke agreement. Now, we’re not going to surrender before we’ve had that battle. We’re going to be having those discussions this week in our committee cabinet," said Rudd, in an effort to paper over a rift in the cabinet.
Junior housing minister Dominic Raab said on Sunday the UK would leave the customs union but that there would be "some customs arrangement dealing".