Darling said: "There is a long-standing anomaly which has meant cider has been under-taxed in comparison with other alcoholic drinks."
As a result, duty increased on Sunday by about 13% accounting for inflation.
Darling added that further increases in the duty on cider over 7.5% abv would follow. "In September changes will be made to the definition of cider to ensure specific strong ciders are taxed more appropriately."
Responding, Merrydown managing director Chris Carr said: "As cider has been enjoying a resurgence in sales, it's obviously disappointing to see it singled out for a significantly higher increase in duty.
"This move could challenge growth levels in the short-term, but with ongoing investment and innovation, cider will continue to flourish in the long run."
Brothers Drinks managing director Matthew Showering warned that a significant price rise "would probably be counterproductive in raising revenue for HMRC".