The South African Revenue Service (Sars) says the shoes are counterfeit Crocs.
Shoprite Checkers says they are not, and wants Sars to return the 10 000 pairs it seized.
Its application to have the shoes returned is expected to be heard in the Cape High Court on Thursday.
The retailer says in court papers that the warrant to seize the consignment had been wrongfully issued and wants the court to set it aside.
It also wants the shoes returned and is seeking damages from the commissioner for customs and excise and Sars officials.
Should Crocs Inc oppose the application, it wants the court to order the US corporation to pay it damages which the court deems fit.
Shoprite Checkers director André van Zyl said in an affidavit that Sars did not have a prima facie case when it applied for the warrant before a Cape Town magistrate.
He claimed the magistrate had not been told the Copyright Act makes provision for the supermarket chain to copy the design of the shoe. This section allows products, having utilitarian purpose, to be copied.
There were serious irregularities about the way the goods had been dealt with and this was not disclosed to the magistrate, Van Zyl said.
Had this been done, the magistrate would not have issued the warrant, Shoprite Checkers submitted.
The retailer had sent letters to Sars disputing allegations that the goods were counterfeit, but these were not placed before the magistrate. This also justified the setting aside of the warrant, Van Zyl said.
Another affidavit contained incorrect information, he alleged.
The application to the magistrate also made no reference to the basis on which the goods were claimed to be counterfeit.
Crocs's Director of Product Development, Erik Olson, said in an affidavit attached to the warrant application that he had examined a sample of the consignment and concluded the shoes were counterfeit because they did not have the Crocs trademark or crocodile device, which the genuine shoe would carry.
The quality of the finishing also did not comply with Crocs's quality requirements.
The sample also featured the word sport on the upper part and the straps were not manufactured from the same material as the rest of the shoe, as is the case with genuine Crocs.
Olson said the beach model shoe is the most popular in the Crocs range and that its shape, configuration and pattern were distinctive.
"Thousands of pairs of Beach model shoes are sold on a monthly basis in South Africa and as such, I am of the view that the Crocs shoe design trademark is known to a substantial number of people in South Africa," said Olson.