An open competition to appoint a new permanent CMO will be held over the summer. Sir Liam's last day will be 31 May, the DoH has said.
Dame Sally is the director general of research and development and chief scientific adviser for the DoH and NHS. She will continue to fulfil these roles until a permanent successor to Sir Liam is announced.
Dame Sally is currently responsible for implementation of the National Institute for Health Research. She is a board member of the Office of the Coordination of Health Research, and chairs the UK Clinical Research Collaboration.
Sir Liam announced his resignation last December. He took up the role in 1998 which makes him the longest serving CMO of modern times.