The education select committee said that they could not endorse the appointment because they felt Ms Atkinson had not shown enough determination to assert the independence of the role.
Mr Balls dismissed the report and Ms Atkinson is to take up the job of children's commissioner on 1 March 2010.
Chair of the education select committee Barry Sheerman branded Mr Balls 'a bit of a bully'. Speaking on Radio 4's 'Today' programme on Monday, he said, 'Maggie Atkinson is a very competent woman but we just didn't think she had the independence of mind to stand up to a secretary of state who likes to get his own way.'
Sir Paul Ennals, chief executive of the National Children's Bureau, who had been on the interview panel, said, 'The children and young people judged her to be the best candidate for the post and the interview panel were unanimous in their recommendation.'