The EU has launched a probe following complaints from UK body Which? It found that UK users paid 79p to download a song, compared with 66p paid by French and German users.
Brussels has written to iTunes and a number of other unnamed record companies to notify them of their objections - the first step in formal proceedings.
European Union competition spokesman Jonathan Todd said consumers can only buy music from the iTunes online stores in their country of residence and are therefore restricted in their choice of where to buy music.
Apple said it had always wanted to offer a fully pan-European service, but was restricted by the demands of its music partners.
Apple said in a statement: 'We were advised by the music labels and publishers that there were certain legal limits to the rights they could grant us.'
The companies under fire from the European Commission inquiry have two months in which to respond to the charges.
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