Jeremy Purvis MSP, the Lib Dem finance spokesman, labelled the SNP policy as being "anti business". The party has lodged a motion to annul the regulations that would see large retailers hit with a business rates hike.
The move comes after a number of business organisations published a letter in Scotland on Sunday yesterday decrying the rates rise as "short sighted" and "counterproductive".
The letter, signed by the Scottish Retail Consortium, the Scottish Chambers of Commerce, the CBI Scotland, the British Council of Shopping Centres, the Scottish Property Federation and the Institute of Directors, also said that the Scottish Government "shoots itself in the foot" with the policy.
Property firm Ryden has also estimated that a number of retailers would be caught in the rates rise, including Debenhams, John Lewis, Marks & Spencer as well as Harvey Nichols. This is despite the SNP's aims to target the levy at supermarket chains and out-of-town superstores.
Purvis, who dubbed the "perverse" rates rise as a "Princess Street Penalty", said: "The SNP is anti business. Ministers are jeopardising our economic recovery with a Princes Street Penalty.
"Already the Scottish Government has refused to help businesses faced with rates tax increases as a result of the revaluation. In England there is transitional relief for businesses in this situation.
"Retailers in Edinburgh and Glasgow are now at a competitive disadvantage from those in Newcastle, Carlisle and Manchester. This is a perverse position to be in with a nationalist government.
"The SNP didn't discuss their plans to hit big retailers with a massive tax hike. They tried to sneak it in the back door. I've started proceedings in the Parliament to force ministers to discuss (this] with retailers and business organisations."