The machines are located in tobacco retail stores that sell customers loose tobacco that they then load into the machines, which roll a carton's worth of cigarettes in about 10 minutes, the Milwaukee Journal Sentinel reported Monday.
Customers pay about $32, around half the cost of premium brands, because they're charged the taxes for pipe tobacco rather than the ones imposed on standard cigarettes.
The Department of Revenue sent letters to owners of the machines informing them they could not operate the machines unless they secured manufacturing and distribution permits and received other administrative approvals.
The department says there are 50 to 100 roll-your-own machines in the state.
Owners of the machines in Wisconsin say the department is overstepping its authorities.
"We're not manufacturing and distributing cigarettes. We're selling loose tobacco," Kurt Kruchten, owner of Smokes-4-Less in Slinger, said.