The software, known as Fairplay, controls the type of music that can be played on the iPod, and to date Apple has been zealous in keeping it secret – effectively restricting the downloaded music playable on the device to that which can be purchased from Apple's iTunes.
A number of on-line digital music retailers have asked Apple for a licence to the technology, so that their music can be played on the iPod, but so far Apple has refused, according to reports.
According to Apple's most recent quarterly filing with the US Securities and Exchange Commission, Virgin made the complaint on 28th June, and is seeking "Interim Measures", pending the merits of the case being decided.
A hearing is not expected until October or November.
News of the complaint comes shortly after digital music company RealNetworks revealed that it had created software that would allow consumers to transfer downloaded music to every popular music device – including the iPod.
Apple and Virgin have made no comment on the complaint as yet.