More than 80 per cent of goods are sold by independent retailers but they are not receiving payments by Amazon.
The glitch also means products sent out for Christmas could be affected.
Hundreds of thousands of Amazon products could be unavailable for Black Friday because a computer glitch
One retailer said: 'If this carries on I'll be out of business in a week.'
One fashion retailer told The Sun: 'I am nearly £15,000 out of pocket at the worst time of the year for cash flow when we are buying in for the December rush. We are on our knees.'
Other customers threatened to take their business to eBay.
Usually, retailers are automatically sent money every two weeks by Amazon, but the system is not currently working for affected retailers.
The internet giant has already launched its online Black Friday Deals Store in the build up to the day of bargain sales.
Other retailers, including Tesco, Argos, Amazon, Currys and John Lewis also slash prices on hundreds of items on Black Friday.
A spokesman for Amazon said: 'We are working to resolve this matter quickly for the small number of sellers affected.'
Black Friday sales on November 24 this year might be affected by the computer glitch