The DJ was abruptly taken off air last week.
He last hosted his show last Tuesday and signed off with: “See you tomorrow.”
Yesterday, a BBC spokesperson said: “While we do not comment on matters relating to individuals, we can confirm Scott Mills is no longer contracted to work with the BBC.”
The allegation relates to a relationship with a male from more than 10 years ago, according to The Mirror.
Representatives for Mills have been contacted for comment.
Veteran DJ Gary Davies replaced him from Wednesday onwards but has not alluded to Mills’ departure.
When he unexpectedly hosted the breakfast show on Wednesday, Davies did not address the reason for Mills’ absence and just…