David Mundell believes Labour voters in Scotland would be “appalled” by the notion of the party forging an alliance with the SNP.
The Tory frontbencher suggested a partnership between the pair at Westminster would render Scottish Labour redundant.
Yesterday, former SNP minister Kenny MacAskill urged the UK Labour leadership to listen to internal calls for a “progressive alliance” with the SNP to evict the Conservatives from government.
He welcomed shadow Scottish secretary Dave Anderson’s comment that Labour should be open to an SNP coalition.
The English MP, who was appointed by Jeremy Corbyn after Ian Murray resigned, provoked a backlash from Scottish Labour when he claimed an SNP deal may be “the price that we have to pay to prevent another rabid right wing Tory government”.
Scottish Labour leader Kezia Dugdale has said a deal with the Nationalists “just wouldn’t work”.
But Mr MacAskill, a longstanding ally of former SNP leader and current foreign affairs spokesman Alex Salmond, described Mr Anderson’s remarks as “sensible”.
He said they “deserve wider support both within his own party and beyond”.
Speaking to the Press and Journal before his visit to Aberdeen, Mr Mundell said: “People who voted Labour in Scotland will be appalled by the suggestion there should be an alliance with the SNP.
“If Labour in England are going to have an alliance, what’s the point in Scottish Labour?
“It reaffirms the view that Ruth Davidson and the Scottish Conservatives are the only opposition to the SNP in Scotland.”
Scottish Labour parliamentary business manager James Kelly hit back, saying Mr Mundell’s time would be better spent “trying to sort out the absolute mess his party has created with Brexit”.
He added: “Many people who voted Conservative at the last Scottish parliament election will be furious that the EU referendum that only the Tories and Ukip wanted has given the SNP the excuse they need to start campaigning for another referendum.
“Scottish Labour have been very clear – we do not back a UK Government deal with the SNP.”