Michael Gove has claimed the refusal of the SNP to back the new Brexit Bill could suggest they want the UK leave the EU without a deal.
The Chancellor of the Duchy of Lancaster, in response to Scottish Conservative MSP Adam Tomkins, said he can understand why people accuse the SNP of quietly supporting no-deal.
Some opposition politicians have claimed the SNP would benefit from the economic downturn predicted following a no-deal exit, with a possible increase in support for Scottish independence, something the party has denied.
Mr Gove made the comments while speaking via video link to the Finance and Constitution Committee at the Scottish Parliament on Monday.
Mr Tomkins asked: "It does raise the question of why all SNP MPs voted against this deal and its predecessor deal on four occasions.
"(Scottish Brexit Secretary) Mr Russell called for a transition period, this deal provides for that.
"Mr Russell also called for no hard border on the island of Ireland and this deal avoids it.
"Nicola Sturgeon called for a guarantee on EU citizens' rights and this deal provides for it.
"Given that this deal provides for so many things that the SNP has rightly demanded, do you understand why the SNP continue to vote against it?
"Is it because they want a no-deal Brexit?"
Mr Gove said: "I certainly don't want a no-deal outcome. The best means of avoiding a no-deal outcome is to vote for this deal.
"The failure of SNP MPs in the House of Commons to vote for this deal so far would allow a lot of people to draw the same conclusions as you have Professor Tomkins, yes."
In September, Scottish Conservative MSP Murdo Fraser wrote in The Scotsman that the SNP "want to make the resulting economic damage worse in the hope of boosting support for independence".