The Large Retailer Levy could yet come into force on 1 April if the Scottish parliament votes it through next week. However, the committee's rejection was seen as an important step towards its annulment.
"The committee has taken a level-headed look at the potential economic impact of this levy and wisely taken the view that it is not in the interests of the Scottish economy or Scottish jobs," said Scottish Retail Consortium director Fiona Moriarty.
"Retail is the engine room of economic recovery and, given the right support, will help Scotland work through the difficult times ahead."
The levy would endanger future jobs growth and investment, she added. "We very much hope the Scottish Parliament will follow suit and vote to prevent it coming into force."
Under the levy, retail properties with a rateable value of at least £750,000 would be charged a supplement. The level would vary according to retail value, but the most valuable properties of more than £2,140,000 could face a supplement of 15p/pound.
The Scottish government argued that more than 90% of the £30m generated would come from big supermarkets or out-of-town retail parks.