EU citizens account for just six percent of the industry's 170,000 workforce, the British Retail Consortium said, BBC reported.
However, they are concentrated in warehouse and distribution jobs, its annual workforce survey showed.
More than half of retailers said their EU employees were worried about their right to remain in the UK.
Just over a fifth of retail firms had had some European staff leave the UK already, the BRC survey found.
The trade body said ending of free movement for EU nationals could lead to higher costs for businesses and consumers, "from the service delivered in a store to next day delivery of an online order to the prices of what you buy".
It argued that the retail sector should keep access to non-graduate European workers without the need for employer sponsorship after the UK leaves the EU.
BRC chief executive Helen Dickinson said the Brexit decision had created uncertainty for both business and their EU workers.
"It is not right that 16 months after the referendum these people still don't have the security they need to continue their lives," she said.
"And from our data it is clear that unless we have the right structures in place to support retailers attract, recruit and retain workers, consumers will soon start to see and feel an impact as they shop."
John Hannett, general secretary of the Union of Shop, Distributive and Allied Workers (USDAW), said: "The sector will continue to need EU workers to come and work in retail, distribution and food manufacturing. We need a debate, based on facts and evidence, as to what that post-Brexit retail sector will look like."
A government spokesperson said: "After we leave the EU we will have an immigration system which works in the best interests of the UK. Crucial to the development of this will be the views from a range of businesses.
"We have asked the Migration Advisory Committee (MAC) to assess the role EU citizens play in the UK economy and society. Their independent process will allow employers to submit their thoughts to an influential group of experts, independent of government."