During Radio 1's Sunday evening show 'Switch', presented by Nick Grimshaw and Annie Mac, Grimshaw asked Barrowman, who has starred in 'Doctor Who' and its spin-off 'Torchwood': "You're famous for getting your willy out in interviews, is this going to happen today?"
Barrowman responded by saying he was going to "get it out", amid shouting and laughter. He was later heard to say: "I didn't take the whole thing out, but I got my fruit and nuts out."
Annie Mac apologised on-air at the end of the programme for any offence that may have been caused. The BBC emphasised that nothing untoward was screened online.
The incident comes hot on the heels of the investigation into the prank phone calls made to Andrew Sachs by Jonathan Ross and Russell Brand, for Brand's Radio 2 show.
The timing could not be worse for BBC management, which just ten days ago, commenting on the Ross and Brand debacle, said it was "determined to act on the lessons learnt from this incident, in particular to reinforce adherence to the BBC's compliance systems. This will be a major priority within the BBC's audio and music division."