The Black Eyed Peas band's frontman tweeted that he was singled out when he missed a plane announcement to put his laptop away.
Qantas issued a statement denying the allegation.
"There was a misunderstanding on board, which seems to have been exacerbated by will.i.am wearing noise cancelling headphones and not being able to hear instructions from crew," a spokesman said.
"We'll be following up with will.i.am and wish him well for the rest of the tour."