Malcolm Whitehouse, programme director for the government's £2.2bn Cinitiative, has stepped down from the role.
Whitehouse is to be replaced by the Department for Work and Pensions (DWP) benefits director Hilary Reynolds and will remain in his position in the short-term to help manage the leadership transition. His next position is yet to be announced.
The move comes amid speculation that a number of senior figures will also depart from the government's flagship benefits reform project - sources suggest that up to five senior project leaders and several contractors are to leave the programme.
A DWP press office spokeswoman said Whitehouse's departure was part of the programme's move from design phase to implementation. She said the department was aiming to bring in new people with different skill sets.
"With the early roll-out of Universal Credit starting in less than six months' time, the programme is moving from system design to delivery. To reflect this, there have been some staff changes as we shift the focus onto implementation," said the spokeswoman.
But previous inquiries into failures of government IT projects have highlighted the importance in leadership continuity during projects, as too often senior civil servants are moved off programmes before they understand the IT complexities involved.
An influential report by the The Public Administration Select Committee last year said: "Wherever possible SROs should stay in post to oversee the delivery of the benefits for which they are accountable and which the project was intended to deliver."
The MPs' report added: "When SROs do move on they should remain accountable for those decisions taken on their watch, and ministers should be held accountable when this does not happen."
Whitehouse has worked within the DWP for nine years, having taken the role as programme director in July 2011.
The DWP is also taking the lead on government's Identity Assurance (IDA) programme, designed to allow citizens to authenticate themselves online using their preferred provider. IDA will play a key part in claimants accessing Universal Credit benefits.
The DWP said there is still no date as to when its IDA supplier framework list will be announced, but said it expects to make an announcement shortly. The list was originally due to be announced on 22 October.
