Most of the vaccines supplied to the Covax scheme, intended to get the jab to poorer countries, have been from India.
The head of the African Union's vaccine delivery programme, Dr Ayoade Alakija, told the BBC's Focus on Africa programme that she hoped the EU exclusion was an administrative error.
But she said she was concerned that "what it feels like here is there's a two-tier vaccine system".
The EU is set to introduce its Digital Covid Certificate on Thursday, but only four vaccines - all made in Western countries - have been approved for inclusion.
