"Auto services should be discontinued and also not to charge passengers more than the fare prescribed by the government," the notice by the department read.
The state government has given three days to the companies to file their reply and a compliance report.
Several commuters had complained to the state government that the companies charge a minimum of Rs 100 as fare even when the distance is below 2 km. According to the norms, the auto drivers are eligible to charge a fixed Rs 30 for the first 2 km and Rs 15 per km thereafter.
The state police authorities also said that these companies are not eligible to run auto-rickshaws as the rules are available for taxis only.
"The aggregators are providing autorickshaw services in violation of government regulations. Also, it has come to the notice of the department that customers are being charged higher rates than the rates fixed by the government," transport commissioner T H M Kumar was quoted as saying by Times Now.
In September, according to Times Now, the state government registered 292 cases on behalf of the citizens, against the ride aggregators for overcharging.
The local auto drivers in Bengaluru were also planning to counter the app-based aggregators by launching their own mobile applications. The "Namma Yatri" app is expected to be launched on November 1.