It had been reported that the track, from recent album A Curious Thing, was written about the murder of the two-year-old in Merseyside in 1993.
Macdonald told DS: "That's a made up story from The Sun - what I said was completely taken out of context.
"When I read what The Sun had written, it totally shocked me because I'd never really been the victim of that kind of thing before."
She added: "It made me feel really terrible because I thought people might get upset by what they thought I'd said.
"Thankfully, the person who wrote it apologised to me. I'm probably one of the only people in the world who can say they've had a Sun journalist apologise to them for writing nonsense!"
> Click here to read our full interview with Amy