The Scottish Secretary claimed he argued against the 10.1 per cent hike, but was “not successful”.
It comes as the Chancellor Jeremy Hunt insisted the industry would still thrive in spite of the increased taxes.
The hike will, according to the Scotch Whisky Association, mean taxes account for 75 per cent of the cost of an average-priced bottle of Scotch, with a £15.22 bottle seeing a total of £11.40 go to the taxman through duty and VAT.
Mr Jack said: “Did I lobby against it, yes I did, did I lobby against it the last few years successfully yes, but this time the lobbying hasn't been successful.”
“It is matter of regret that whisky duty, spirits duty is going up, it's not what I wanted for the Scottish industry'”
He has now been accused of failing by the Lib Dem MP Alistair Carmichael, who claimed he’d managed to protect the industry during coalition.
The Orkney and Shetland MP said: “Alister Jack’s admission that he tried and failed is a colossal failure of politics. He tries to disavow the policy but cling to office. It is not clear how he can do this or even why. What is the point of being in a job like that if you cannot deliver?“This was meant to be a budget for growth so the case for cancelling the duty rise on Scotch whisky ought to make itself. This is one of the few successful manufacturing sectors we have left. It has the capacity to deliver the growth we need, especially in export markets. Instead it gets clobbered by a government which has prioritised massive bungs to their mates in the city while using doctors as a human shield.“I know that it is not easy to make a case with Treasury for tax cuts, but Danny Alexander and I did exactly that in 2015. We won the argument. That Alister Jack cannot even deliver a freeze should be a source of shame for Scottish Conservatives."
Mark Kent, chief executive of the SWA, is now demanding an urgent meeting with the Chancellor to discuss the impact of the changes.
He called for the duty rise to be reversed, telling Mr Hunt: “With the right support, with a reversal of the tax rise, we are confident the industry can continue to deliver for the UK economy.”
However Mr Hunt insisted the Government is keeping duty levels low, with his approach “beneficial to whisky distillers”.
Speaking on BBC Radio Scotland’s Good Morning Scotland programme, the Chancellor said: “We have been working very closely with the Scotch Whisky Association and we have frozen alcohol duty until August.
“In real terms this means we will have the lowest level of duty for over 100 years, so we are keeping duty levels low.
“We will continue to engage with the industry and we want to do something that will mean they are successful and prosperous going forward.”
The Scotsman understands Mr Jack believes trade agreements for scotch, in areas such as India, will be far more beneficial to the sector, and believe Scottish Government plans to ban alcohol advertising are more dangerous to the industry.