The budget airline is not passing on all the money it collects from the charge to the Dublin Airport Authority (DAA), and said that the levy is too high.
The DAA has imposed a fee of 33c per departing passenger since July.
This follows an EU directive obliging all travellers to pay their share of the cost of services for the disabled at airports.
However, Ryanair is continuing to charge all its passengers a standard wheelchair levy of 50c.
Passengers using Cork and Shannon are also charged a wheelchair levy of 50c, despite the fact that the charge set by the DAA at these airports is 45c.
It was revealed in August that Ryanair passengers at Cork Airport were being charged more than €15 per head in "taxes and fees" that the airline does not have to pay.
The airport charges only apply to routes a year after their introduction.
However, the budget airline was charging customers travelling on the eight-month-old Glasgow and East Midlands routes.
Aviation sources told the Irish Examiner newspaper today that Ryanair, which has now axed these two routes, was turning a huge profit by charging consumers for the costs.
The Ryanair website broke down a €24.12 add-on as €18.13 in taxes and fees and €5.99 in "insurance/wheelchair levy/aviation insurance".
This meant that, after deducting the €2.50 security charge, the company is still charging an extra €15.63.
The airline said at the time: "In most cases, passengers travelling from Cork will not pay any taxes and charges as Ryanair absorbs these costs in order to make these routes attractive."
Ryanair is currently involved in a high-profile takeover bid of Aer Lingus.
Ryanair accounts for an estimated 8pc of Europe's internal airline market, but its share of the low-fares sector is around 40pc.
Though the carrier is still growing passenger volume, it is forecast that in its financial year ending March 2009, the airline will post a net loss of €140m compared to a profit of €390m last year.
The alarming swing into the red is largely due to increased fuel prices.