According to the BBC, the band had been due to play a headline slot at the Summer Sundae Weekender in Leicester tonight. They have also scrapped a show at the Picture House in Edinburgh.
The 30-year-old rapper announced the news via his Twitter page, saying: "Just as I get the all clear, my bass player Wayney is diagnosed with swine flu."
A message posted a few hours earlier said that he was "waiting to hear from management" about whether the concerts would take place.
Skinner added: "But I suspect this weekend is not going to happen. I want to cry for socialist and capitalist reasons."
The musician had previously posted a track online titled 'He's Behind You, He's Got Swine Flu', featuring the same bassist who is now suffering from the illness.
"Listen to the bass line of this song and spare a thought for the guy who played it, suffering with the terrible virus," he said.
Scottish rockers Idlewild have now been moved up the bill and will close the main stage instead, a spokesperson for the Summer Sundae Weekender has since confirmed.