A spokeswoman denied that her decision to quit was because she had been "kept in the dark" over the business dealings of David Mills, the estranged husband of Tessa Jowell.
The Mail on Sunday reported last night that Dame Sue, the most senior civil servant in Ms Jowell's department, had had a series of clashes with the Culture Secretary over the activities of David Mills.
It said relations between the two women became strained over Ms Jowell's failure to register two of Mr Mills's business deals.
But a spokeswoman for the Department of Culture said: "To suggest that there has been a series of stand- up rows is completely untrue. She is leaving for her own personal reasons and came to the end of her four- year stint in December. She gave the department six months notice within the last couple of weeks."
The Department of Culture posted the announcement of Dame Sue's departure on its website on Friday afternoon. It said the 56-year-old senior civil servant was taking "early retirement", and added: "Dame Sue will retire in September. After a few weeks' break she intends to undertake a portfolio of work in the public and private sectors."
Dame Sue said in a statement she "couldn't be more proud of my colleagues. It has been a privilege to work with them, with Tessa Jowell and her team, and with the world-class organisations we sponsor."
Her sudden exit will be a huge blow to Sir Gus O'Donnell, Whitehall's most senior civil servant, who has promised to appoint more women to senior roles.
With Dame Sue's departure, it means there will now be only one female Permanent Secretary left in Whitehall. She is Helen Ghosh who is at the Department for Environment, Food and Rural Affairs.Reuse content