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 told listeners: “Morning, Gary in for Scott.”
News of Mills’ sacking led yesterday’s noon bulletin on his former station BBC Radio 2.
At the start of his own Radio 2 show, Jeremy Vine said he was “taken aback” by the news.
BBC presenter Scott Mills. Photo: Jonathan Brady/PA
Today’s news in 90 Seconds – Tuesday, March 31
He added: “I had not heard anything about it until 17 minutes ago, when it was on the BBC website and I only had the information that was given to you in the bulletin, I have nothing more, that it was allegations about Scott Mills’ personal conduct, which have led to him being sacked.
“I have no more than that. All right, on to today’s show.”
In an email sent to staff, Lorna Clarke, director of music, wrote: “I wanted to personally let you know that Scott Mills has left the breakfast show, and the BBC.
“I know that this news will be sudden and unexpected and therefore must come as a shock. Not least as so many of us have worked with Scott over a great many years, across a broad range of our programmes on R1, 5Live, R2 and TV.
“I felt it was important to share this news with you at the earliest opportunity.
I hope you can understand that I am not going to be saying anything further now
“Of course, it will also come as a shock to our audience and loyal breakfast show listeners too. I will update everyone with more information on plans for the show when I’m able to.
“While I appreciate many of you will have questions, I hope you can understand that I am not going to be saying anything further now.”
The 53-year-old from Southampton took over the breakfast show from Zoe Ball last year.
The latest Rajar figures in February showed Mills had an average weekly audience of 6.47 million between October and December 2025, up from 6.16 million the previous quarter and his highest figure since taking over the Radio 2 breakfast show.
The BBC annual report in July 2025 revealed he earned between £355,000 (€408,390) and £359,999 a year.
Mills began his BBC career on Radio 1 in the late 1990s as the early breakfast host, before going on to present weekend slots and then an early evening show while providing maternity cover for Sara Cox.
When Cox did not return, the programme was renamed The Scott Mills Show.
In 2022, he joined Radio 2, replacing Steve Wright in his weekday afternoon slot.
He has presented a number of shows on the station before taking up the Breakfast Show after Ball’s departure.
Mills has also presented a weekend show on Radio 5 Live and appeared on series 12 of Strictly Come Dancing.
He is due to support Boyzone on their Two for the Road gigs in June.