The Universal Credit welfare programme could face further delays because of friction between the Department of Work and Pensions (DWP) and the Cabinet Office.
There are now "high-level" risks to the delivery of the project, according to minutes of a Whitehall meeting, which were leaked to The Guardian newspaper.
Cabinet Office minister Francis Maude is said to have pulled out many of the department's IT experts from the Government Digital Service (GDS) from the project because of tensions rising over the lack of progress of the project.
Back in December, in a briefing with Computing and other media, Maude had complimented the staff working on Universal Credit, adding that there were "inconsistencies" across the whole of government.
"I would say that the team that has developed the exemplar digital solution - what everyone sees as the strategic long-term answer to Universal Credit, has been predominantly a DWP team with some really terrific people and this will be taken forward by DWP.
"This is never about the solutions being provided exclusively by the GDS, it is GDS working with in-house teams very creatively, bringing in outside contractors and developers to work intensively with the department," he said.
"The DWP team working on digital has GDS team members in there, and in the space of three months they developed the spine - a relatively thin spine - but a digital solution, and that will be developed on," he added.
But according to the leaked minutes, DWP now has to look for new IT specialists to keep the project moving, and this could lead to further delays and more of the DWP's budget spent on the project.
Tension is believed to have risen to an all-time high, when the secretary of state for work and pensions, Iain Duncan Smith, who has led the Universal Credit programme, is thought to have rebuffed calls by other government officials for the project to be restarted.
This was after DWP had to write off millions of pounds, endure several delays and be accused by a former employee of its team of only worrying about "asking what the Daily Mail says if they hear about it".
Another leaked document obtained by the Guardian, claimed that the DWP may not be "able to obtain the skills required to replace GDS within the current market at affordable cost".
Howard Shiplee, now in charge of the project is quoting as being "disappointed" during the meeting.
The leaked board minutes state: "GDS wished to accelerate their withdrawal from the design-and-build team to allow DWP to take ownership.
"However, as GDS have supplied most of the expertise and resource to date, and a recruitment exercise needs to be undertaken to fill the technical vacancies, there is therefore the likelihood of some delay."
Another senior civil servant said that "friction between DWP and Cabinet Office" made things more "difficult than necessary".