Tickets for the event first went on sale in October last year with deposits of £50 being paid for the £195 passes.
Unwanted and unsold passes went on resale at 9am.
The festival apologised via their GlastoFest Twitter account to those who did not get a ticket, saying "demand hugely outstripped supply".
The event at Worthy Farm in Somerset, which starts on 22 June, has 137,500 public tickets.
Headline acts will be U2, Coldplay and Beyonce.