The Conservative MP, who is one of the party’s most hard line Brexiteers, made the comments as he arrived in Scotland on a short speaking tour.
He said he agreed with Alex Salmond’s previous view that the 2014 vote on Scottish independence was a “once in a generation” decision which should not be revisited in the short term.
“Of course Scotland is entitled to have another referendum at some point in the future, but I think the SNP’s position of a ‘generation’ is a reasonable one – that it should be a generational decision,” he told the BBC.
“A generational decision is not one made over two or three years.”
He added that 20 years was a more realistic timeframe for another vote on Scottish independence, meaning that it would not take place until nearly 2040.
Mr Rees-Mogg also said he was in favour of more powers being devolved to Scotland in the wake of Brexit, but not over the key areas of trade or immigration.
Mr Salmond’s made his “once in a generation” comments four days before 2014’s referendum, which saw Scots reject independence by a margin of 55 per cent to 45 per cent.
However, he has since said that this was only an “estimation” based on the periods between previous constitutional votes and that the seismic political events since 2014 had changed matters.
Nicola Sturgeon is set to update MSPs at the Scottish Parliament on her plans for another vote in the next few months, after postponing them following last year’s snap general election.
Despite their different political backgrounds, Mr Rees-Mogg also praised the Scottish Tory leader Ruth Davidson, tipping her as a future leader of the UK party.
“I think Ruth Davidson is a brilliant, charismatic and capable political figure, I admire her hugely,” he said.
“She will at some future date make a wonderful leader, both as First Minister in Scotland and in due course leader of the Conservative Party in England. She is a wonderfully capable person.”
An SNP spokeswoman said: “The fact that right-wing, extreme Brexiteer Tories like Jacob Rees-Mogg are seeking to dictate to the people of Scotland shows exactly why decisions about Scotland should be taken in Scotland and not at Westminster.
“The SNP’s 2016 manifesto clearly set out the case for a second independence referendum if there was a ‘significant material change in circumstances that prevailed in 2014, such as Scotland being taken out of the EU against our will’ – a position that has subsequently been backed by a majority of MSPs in the Scottish Parliament.
“As the deeply damaging consequences of Brexit become clearer, and as Scotland’s economy continues to outperform the UK, it’s no wonder that people like Jacob Rees-Mogg are rattled at the prospect of people once again discussing the immense opportunities of Scottish independence.”