The government is proposing a national pension scheme for those without access to occupational pensions, who would be automatically enrolled onto either their employer's scheme or a new personal account.
Under the plans, employers would pay contributions of 3% of employees' salary, although staff could opt out.
However, the Association of Convenience Stores believes the scheme would add an extra 1% to wage costs.
ACS chief executive David Rae said: "Taken alongside the rapid increases we have seen in the National Minimum Wage and the extension of paid holiday entitlement, the proposals represent a significant cost burden to local shops."
He added: "We are asking retailers to make their voice heard now, or they risk being ignored in this critical debate."
The ACS has criticised the government's lack of detailed research into the costs for the convenience store sector and says although there is an assumption that 20-50% of employees will opt out of the pension scheme, it is not clear how this would apply to small shops.
Retailers who want to express their views on the scheme's impact should contact the ACS before the government's consultation closes on September 11.