The Brexiteer MP, a key figure in Boris Johnson's government, launched a tirade at SNP MP Pete Wishart.
Mr Rees-Mogg said: "What we have seen today is I think in history unprecedented, unknown, unseen - a frightened Scotsman. They are people know for their courage, forthrightness and their sturdiness and they are scared of going in front of their own voters.
"They have run away from an election, they are timorous beasties."
The remarks came as the row over whether or not to hold a general election to break the parliamentary deadlock over Brexit rumbled on.
The SNP have made their position clear. They want to use legislation to block the possibility of a No Deal Brexit, then go to the polls.
Mr Rees-Mogg and the Prime Minister, on the other hand, want to use a general election to win a majority and push on with a hard Brexit.
Mr Wishart said the Leader of the House wanted to 'contemptuously' suspend democracy and mocked Mr Rees-Mogg for lying down on the Commons benches.
The row comes as Mr Rees-Mogg is criticised for his mockery of a doctor who advised the government about the impact of a No Deal Brexit.
Mr Rees-Mogg likened Dr David Nicholl to Dr Andrew Wakefield, the discredited medic at the heart of the anti-vaccine movement.
The British Medical Association has condemned the remarks and the Prime Minister has distanced himself from Mr Rees-Mogg's position.