She had been expected to present an award at the show in Edinburgh on Thursday.
But organisers have confirmed that ill health has meant the pop princess won't be turning up.
Huge stars like Beyonce, Kylie and the White Stripes are all performing live at the awards ceremony in Scotland.
An MTV spokeswoman said: "Britney was due to present an award as opposed to perform but has pulled out due to ill health.
"We are disappointed she won't be attending but we wish her well for a speedy recovery.
"We are still looking forward to a fantastic show on Thursday."
The spokeswoman could not comment on news reports that Britney is suffering from flu.
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