Nine out of 10 independent store owners surveyed have seen their business hit by bootlegging in the last year, the study found.
The problem has cost the average retailer pounds 1,293 a week, a total of pounds 67,236 a year, according to the survey by Independent Retail News magazine and the Booker cash and carry chain, which questioned more than 500 independent retailers.
While it is a national phenomenon which costs the Government pounds 1bn a year in revenue evasion, bootlegging affects some areas far more than others, the study showed.
In the north-east, retailers have seen more than a third of their tobacco sales disappear in the past 12 months, with overall trade down 18 per cent. In the London area overall trade is down an average 21 per cent, while in central England the average trade losses are 19 per cent.
Across the UK the average loss of business attributed by retailers to bootlegging in the past year was 16.6 per cent, with 54 per cent of retailers saying they had lost up to a quarter of their takings and 35 per cent who lost between 6 and 20 per cent. Based on figures for the UK average store turnover, these losses total pounds 3.16 billion.
Bootlegged goods are sold out of the back of vans, from pubs, clubs, private houses, door-to-door hawkers, building sites, factories, taxis and ice cream vans, the survey found.
Richard Siddle, editor of Independent Retail News, said: "Bootlegging is quite simply big business for criminals and while the Government may moan it costs them pounds 1bn a year in revenue evasion it is doing little to dent the bootleggers' activities. After all the pounds 1bn it loses is more than made up in the billions of pounds it receives from its annual cigarette and alcohol tax hikes."
The publication is launching an action week next Monday. It will tell retailers how to spot bootlegged goods and invite them to call a special Customs and Excise hotline.