Constitution minister Michael Russell said this was "untenable" after Tory leader David Cameron said he would not stand in the way of a referendum on greater powers for the Welsh Assembly.
The Tories rejected the claims and insisted Mr Cameron would back an independence vote in Scotland - if it was passed at Holyrood.
But Mr Russell said: "The Tories are utter hypocrites, and this shows them up in their true colours as opposing Scottish aspirations.
"The Tories support referendums on Europe, and a referendum on more powers for Wales, yet they oppose a free and fair vote to enable the people of Scotland to choose our constitutional future. Their position is untenable.
"David Cameron's Welsh 'leek' has left the Scottish Tories looking like prize neeps."
The Nationalist Government in Scotland is hoping to hold an independence poll next year, but it looks doomed to fail, after the Lib Dems last week re-affirmed their opposition.
That leaves the main opposition parties at Holyrood - along with the Tories and Labour - against a referendum and they all appear set to vote it down when it comes before Parliament.
But a Tory spokesman today accused the SNP of talking "complete nonsense" on the issue.
He said: "There is no inconsistency. There is no contradiction.
"If a majority of the Parliament voted for a referendum then we would not stand in the way.
"But there is no majority for a referendum - it is not on the agenda."
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