The Smile singer was said to have complained about Courtney's company in a message to one of her online friends, joking that a night with the musician made her realise why Kurt Cobain killed himself.
However, Lily has claimed that her Myspace profile was hacked into and she was not responsible for the spiteful message.
Responding on her own Myspace profile, Courtney said: "Thanks to Lily Allen for her lovely apologising for having had her MySpace broken into. I wouldn't pick on me if I was Miss Lily, as it wouldn't take TOO much to swat, but we've known each other far too long, like each other far too much and if she was gonna say something nasty she has the acerbic wit and intelligence to say something cutting, that would actually really hurt, not some cliched hoary old chestnut some obsessed blogger would say."
She added: "She tells me her MySpace was broken into - even if I REALLY think she did blog it mindlessly some 8am after being up far too long for a young healthy woman I don't care and I appreciate and accept her thoughtfulness for apologising for what was printed, if she is telling the truth and it really doesn't much matter - everyone slams everyone early in their careers, (Sonic Youth)'s Kim Gordon still slams me, I mean how much more boring can you get? (than Kim Gordon - slam!) Does anyone care?"