The department seeks to impose a registration and negative licensing scheme, as well as Fixed Penalty Notices and much higher fines for those caught selling to under-18s.
John McKeown from Ballymena has written to more than 1,000 fellow independent retailers across Northern Ireland urging them to make their concerns known before the deadline on March 12.
"Retailers who repeatedly sell to under-18s should be prosecuted, but a licensing scheme would unnecessarily add to an already heavy burden of red tape on responsible retailers," he said.
Store owners are also concerned about plans to ban tobacco displays this summer up to three years before the rest of the UK. John said the move, which is being considered by the Northern Ireland Assembly, would lead to an upsurge in the illicit trade, as being experienced by the Republic of Ireland.