Amanda Lampe has resigned and will leave her position at the end of March to be replaced by Julia Gillard's former chief of staff, Ben Hubbard.
Ms Lampe's performance during last year's federal election campaign is understood to have been criticised by some Labor figures who believed Ms Gillard received poor advice.
But Leader of the House Anthony Albanese has denied the claims.
"Certainly not. I think there's been some chatter in the media as there always is, particularly over the Christmas season," he said.
Mr Albanese says Ms Lampe has chosen to move on from what is a high-pressure job.
"Amanda Lampe is an experienced staffer. She's been a senior staffer here in Canberra to Julia Gillard, but also I worked with Amanda many years ago in Bob Carr's office when he was premier of New South Wales," he said.
"She is widely respected across the party, in the caucus, and I think amongst her fellow staffers.
"She'll be a big loss, but people wish her well."