This follows allegations that the airport offers Ryanair reduced airport charges for existing destinations and new scheduled flights.
The commission says the discounts could be up to 31% for existing destinations and 48% for new services.
But the commission says that, in spite of requests, it has not been provided with the text of the agreement. It says Bratislava Airport has so far refused to comply with a request for a copy of the deal.
'Without access to this document, and on the basis of the information provided by the complainant, the Commission has doubts about its compatibility with EU rules on State aid,' said the commission.
The European Commission ruled in 2004 that some of the state aid paid to Ryanair by the publicly-owned airport in Charleroi, south of the Belgian capital Brussels, was illegal.
Ryanair criticises London air charge plans
Separately, Ryanair has joined a number of other airlines in criticising a new price regime that will drive up fares at the UK's two busiest airports, Heathrow and Gatwick.
The Civil Aviation Authority has announced that the airport operator, the British Airports Authority, can substantially increase the landing fees it charges airlines over the next five years.
This is expected to lead to airlines passing on some of the increase to passengers.
Today's announcement covers the period from April 2008 to the end of March 2013.
The CAA said BAA could increase charges at Heathrow in 2008/09 by 23.5% compared with the charges over the last five years, while the increase at Gatwick will be 21%.
Airlines say the new increases will see Heathrow passengers pay, on average, 17% more than Britain's Competition Commission recommended last September 2007.
