Authorities seized over 90,000 cigarettes and 3.5kg of rolling tobacco during raids on premises in Portland Street in the city in February and August 2020.
The raids were all part of Operation Buckhorn, a joint venture between Lincolnshire County Council's Trading Standards, Lincolnshire Police, and HMRC.
During the first raid on 26 February 2020, officers seized 50,000 cigarettes and 2kg of hand rolling tobacco from five stores known to be selling illicit tobacco on Portland Street.
On 20 August, three of the five shops were raided again by officers from Trading Standards and the police, when a further 40,000 cigarettes and 1.5kg of rolling tobacco were seized. One arrest was made.
In one store, sniffer dogs alerted officers to the illegal cigarettes hidden in three secret compartments behind a wall in a toilet. In another, officers discovered the illegal products hidden in a compartment with a magnetic lock when they noticed the grouting on one section of a tiled wall was a different colour.
Trading Standards investigations continue to bring prosecutions against the retailers.
Andy Wright, Principal Trading Standards Officer, said: "The availability of illegal tobacco acts as a magnet attracting anti-social behaviour and other crime to an area. We are pleased to be working with Lincolnshire Police to tackle this problem on Portland Street and feel we've already made a significant difference.
"After the initial raid on five shops in February, Trading Standards contacted each of the shop landlords. I am delighted to say that in two cases, the landlords took immediate action and evicted problem tenants and there has been no repetition.
"Last week, on 20 August, the remaining three premises were raided again and further evidence found of illicit tobacco selling.
"We're keen to continue to work with premises landlords to bring an end to this illegal activity, and I believe two are already seeking to take legal action against tenants. With their help we could soon see the selling of illegal cigarettes on Portland Street as a thing of the past.
"We will of course monitor the situation closely and take action where we feel landlords are not taking their responsibilities seriously."
Acting Inspector Phil Elliot of Lincolnshire Police, added: "Operation Buckhorn has been a really successful joint project run between Trading Standards, Lincolnshire Police and HMRC to disrupt illicit sales of cigarettes at shops on Portland Street in Lincoln.
"There have been two successful days of action this year, culminating in thousands of illicit cigarettes and several kilos of illicit tobacco being seized and prosecutions being commenced against shop workers.
"The ultimate goal of the operation is to stop the illegal practices at the shops on a permanent basis because it was identified that young people were being drawn to the shops to purchase these illicit cigarettes exposing them to significant risks.
"Improving the safety of children in the area has been the main concern of all agencies and I truly believe this has been achieved. I am really thankful for the enthusiasm and dedication shown by the teams from all three agencies, leading to such positive results that should have a long lasting effect.”