The cost of a research council project to pool back-office functions could rise to more than £130 million - more than double the amount set out in the original business case.
There are also concerns that the scheme's promised efficiency savings are unlikely to be delivered.
The Research Councils UK Shared Service Centre (SSC) is an ambitious plan to increase the councils' operational efficiency by providing joint services.
The full business case approved in 2007 states that administrative functions including finance, human resources, IT and procurement would be pooled by March 2009. Grant processing was scheduled to be incorporated by the end of 2009.
The confidential document, seen by Times Higher Education, sets the project's total implementation costs at just under £55 million and states that in the "worst-case" scenario, this could rise by 40 per cent.
It predicts that savings worth £450 million would be delivered over ten years, excluding implementation costs. More than £400 million of this was supposed to come from procurement.
Yet an update obtained from RCUK reveals vastly increased costs and lower than expected savings.
So far, only four councils have pooled their back-office functions, and joint grant-application processing will not start until later this year.
Despite these setbacks, it is the scheme's spiralling costs that have caused the greatest concern.
In December 2009, RCUK was quoted by magazine Private Eye as saying that the planned cost of the project was £120 million.
But the figure for the final projected costs provided to THE is £125.5 million - with a further £7 million available for contingency funding.
A spokeswoman for RCUK said the project was "on track" to be delivered within the £125.5 million budget.
"As with anything of this nature, there have been challenges ... however, they have been met and overall we consider the establishment of the SSC a success," she said.
The soaring costs have caused disquiet among physicists and astronomers, whose research budgets are being slashed and who fear further cuts to science funding.
There is also concern that the efficiency targets set in 2007 were far too ambitious.
While RCUK told THE that the project was expected to deliver the savings originally planned, some have warned that this will be difficult to achieve, as the large purchases made by the research councils tended to be so specialised.
Delays in implementing the SSC will also leave some councils funding both the old and new systems simultaneously.
One research council source, who asked to remain anonymous, said RCUK had "blown the budget for implementation spectacularly".
"Why weren't more queries about the figures in the business case raised at the time?" they added.
RCUK said the 2007 business case was out of date, and that £24.3 million operating costs were included in the revised figures.