Angus Robertson, the Scottish National Party's Westminster leader, said Mr Carmichael previously campaigned against "discriminatory" duty on whisky but was now supporting it in Government.
Mr Carmichael hit back by suggesting the SNP's support for independence would ruin the whisky industry north of the Border.
During Scotland questions, Mr Robertson told the Scottish Secretary: "In opposition, you and I and others lobbied the Treasury to end duty discrimination. In fact, you tabled an amendment in the Commons to end tax discrimination.
"But since becoming Scottish Secretary you have taken the Tory shilling, you are letting the industry down and you are supporting discriminatory duty."
Mr Carmichael replied: "There is no escaping the fundamental truth that you have got a policy that would be the ruination of the Scotch whisky industry."
Liberal Democrat MP Alan Reid (Argyll and Bute) said it was unfair whisky is taxed at a higher rate when compared to beer and wine.
Mr Carmichael said: "I am sure (Chancellor George Osborne) will always listen to representations from the Scotch whisky industry"