Michael Gove has claimed the refusal of the SNP to back the new Brexit Bill could suggest they want the UK to leave the EU without a deal.
The cabinet minister said he could understand why people accused the party of quietly supporting no deal.
Mr Gove made the comments while speaking via video link to Holyrood’s finance and constitution committee.
Speaking after the meeting, SNP MSP Tom Arthur branded the claims “self-evidently ludicrous”.
Some politicians have claimed a no-deal exit would increase support for independence.
It has also been suggested that the SNP could benefit from the predicated economic downturn.
Earlier, the first ministers of Scotland and Wales said Brexit must be extended so the Welsh Assembly and Scottish Parliament could scrutinise Boris Johnson’s withdrawal deal.
Both will need to vote on a law to implement the deal but Nicola Sturgeon and Mark Drakeford have said 10 days is not enough to consider the legislation.
During the committee hearing at Holyrood, Scottish Conservative MSP Adam Tomkins asked Mr Gove whether the party’s voting record was a cause of concern.
Prof Tomkins said: “It does raise the question of why all SNP MPs voted against this deal and its predecessor deal on four occasions.”
He highlighted the fact that the new deal had a built-in transition period and avoided a hard border on Ireland.
Prof Tomkins added: “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 replied: “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.”
Mr Arthur later rubbished the claims.
He said: “The SNP has been the strongest advocate for remaining in the EU – working round the clock to stop Brexit and protect the interests of the Scottish people, who voted overwhelmingly to stay in the EU.”
Scottish Greens co-leader Patrick Harvie accused the government of double standards.
He said: “Michael Gove has talked about the importance of a consent mechanism for Northern Ireland, but he has confirmed that the UK is utterly unwilling to accept any similar principle for Scotland.
“The level of contempt for Scotland’s interests, and for our constitutional status, is breathtaking.”
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”.