The Songs of Praise star has been taken off the air by the BBC after being accused of sexual harassment.
The former angelic choirboy, 46, faces an allegation of inappropriate behaviour from a female colleague.
The married father of two, 46, who shot to fame as a choirboy in the 1980s, is believed to be one of 25 “live cases” being investigated by the Beeb.
The allegation is believed to centre around messages and contact.
The star — who has not appeared on the BBC since last month — said sorry for his “juvenile” behaviour but denied any inappropriate contact.
A well-placed source told The Sun on Sunday: “There is an allegation that inappropriate messages and contact with a female member of staff took place.
“He’s been told by the BBC about the complaint and after it came to light he has been taken off air.”
It is believed to be one of 25 live cases of alleged sexual harassment recently highlighted by BBC deputy director-general Anne Bulford.
A spokesperson for Jones said: “Although not related to any broadcast work, Aled voluntarily agreed not to go on the BBC whilst the matter is investigated.
“Whilst he accepts that his behaviour over a decade ago was occasionally juvenile, as was that of others, he never intended to harass or distress and he strongly denies any inappropriate contact.
“He is, however, deeply sorry for any upset caused and hopes this matter is resolved soon.”
Aled’s last appearance on his BBC Radio Wales show was on October 22. The previous week he hosted Songs Of Praise from the Welsh town of Pontypridd but has not presented it since.
Jones, who was pictured jumping on the back of a motorbike taxi yesterday, became a household name when Walking In The Air, below, got to No 5 in the charts in 1985.
By the age of 16 he had sold more than six million albums and performed in front of the Pope, the Queen and Princess Diana.
The star, made an MBE in 2013, also hit No 1 in the classical charts with his latest album. On November 3 he tweeted his thanks for the “lovely comments” about his success before adding he had “been really sick — hopefully getting better”.
Jones, who lives in a £1.8million house in Barnes, South West London, with his wife Claire Fossett, has admitted he struggles with his image.
In 2012 he said: “It’s a bit odd people still think I’m squeaky clean.” He acknowledged it “went with the territory” when he was a schoolboy chorister but added: “I’m really just a normal bloke.”
The latest allegation comes as the BBC finds itself caught in the firestorm sparked by the Harvey Weinstein Hollywood sex scandal.
Last week it axed an Agatha Christie drama from its Christmas schedule after British actor Ed Westwick was accused of rape. He has denied all the claims against him.
A BBC spokesman said of Jones: “It is not something that we are going to comment on.”