According to the Mirror, there were 1,569 recorded cases of shoplifting in the city over a 12 month period up to June 2015.
The figures equate to one crime for every 61 residents.
Lincolnshire Police said the data does not account for the large number of people visiting the city.
Ch Insp Stuart Brinn said: "Any shoplifting is a problem - but Lincoln is not a hotbed of shoplifting crime.
"The number of offences in Lincoln is fairly low - what they have looked at is the resident population," he said.
"You divide one by the other and you come up with a relatively high figure."
He added the figures were skewed because groups such as outside workers, students and tourists were not included.
Police said the number of thefts from shops in Lincoln had fallen by 20% since 2013.
Westminster came second in the Mirror's report - with the equivalent of one in every 62 people committing the crime.
Other "shoplifting hotspots" identified in the report include Middlesbrough, Hull, North East Lincolnshire and Nottingham.
South Cambridgeshire had the lowest level of shoplifting crime - according to the report - with just one in every 1,207 people shoplifting over the same period.
Across England and Wales there were 327,925 cases of shoplifting, the Mirror said.  A rate of one crime for every 176 residents.
Police have dismissed claims made by a national newspaper that Lincoln is the shoplifting capital of England and Wales.