The flight has just taken off with only cargo on board, and 44 passengers have been left stranded in transit at Schiphol Airport as a result," she said on Friday.
Reinhard Arndt, one of the 44 passengers, travelled from London to make the flight, and had already spent 26 hours in the airport before the cancellation.
Arndt said that passengers had paid around €950 for the flight and had been cleared by both the Department of International Relations and Cooperation (Dirco) and the relevant High Commissions in the UK and the Netherlands.
According to Schafer, some passengers were told there were not enough quarantine beds available for returning South Africans in Cape Town.
Arndt and other passengers will now be accommodated on a flight leaving Amsterdam later on Saturday, but this flight will land in Johannesburg where passengers will be quarantined before having to make their own way to Cape Town.
