The Manchester Evening News revealed Transport for Greater Manchester (TfGM) is considering a £20m plan for zones in Manchester, Bolton and Bury.
It follows the publication of the  government's draft UK Air Quality Plan.
TfGM said it was "exploring the feasibility" of clean air zones, alongside other options.
Alongside the fee for drivers, the scheme could also see vans charged £20 and lorries £100 to travel in the clean air zones.
The suggested zones - Manchester's inner relief road, the Mancunian Way, Bolton's St Peter's Way and routes south of Bury town centre - would operate 24 hours a day and come into force by 2020.
A TfGM spokesman said it was working closely with the Department for the Environment, Food & Rural Affairs (Defra) on improving air quality by reducing nitrogen dioxide levels.
He said the work was "critical" as Defra's draft report stated it will be the responsibility of local authorities "to bring pollution levels within the legal limits within the shortest time possible".
He added TfGM would be be reviewing Defra's proposals "over the coming weeks".
The UK has struggled to keep within EU limits on some pollutants, particularly nitrogen dioxide (NO2), which is produced by diesel engines and is linked to a range of respiratory diseases, including asthma.
Only six of the 43 regions of the UK are within NO2 limits.
Car drivers in Greater Manchester could face a £7.50 daily congestion charge under plans being considered to meet the government's clean air targets.