The inquiry into the outbreak at the Vale of Leven Hospital, West Dunbartonshire, started in 2009 and was initially expected to cost £4m.
However, the bill has now risen to £9.9m and the report has yet to be published.
Lord MacLean's inquiry is looking into the deaths of 31 patients at the hospital. They died between December 2007 and June 2008. C.diff was said to be the main cause in 28 of the deaths.
The Scottish Government said the full costs would be published once the inquiry had reported.
The inquiry team said a publication date would be announced shortly.