Almost £34m of an operational contingency fund that contained £42.3m at the beginning of last year has gone, two months before the Glasgow 2014 games start.
It was set up to pay for "known and unforeseen cost pressures".
With costs to increase as the 12-day sporting spectacle approaches, Glasgow 2014 has conceded that a separate £24m Scottish Government "special reserve" pot, which was set aside for use only in "exceptional circumstances", may also be used.
The committee was urged last year at a meeting of the Games strategic group, which includes First Minister Alex Salmond, to avoid the need to make further calls on the fund. It had previously been hoped it would not be used at all. Despite that, a further £5m from the fund has been spent over the past three months, leaving just £8.5m.
The fund has been recently used to pay for a shuttle bus service for athletes to Glasgow city centre, better gym facilities for competitors and improving surfacing for wheelchair users.
It has also helped cover spiralling costs of the opening and closing ceremonies, which it emerged had risen from an initial estimate of £14m in late 2012 to almost £21m by last month.
Conservative sport spokeswoman Liz Smith MSP said the more the fund was raided, the less credible the Government's claims that the games were on budget became. She said: "It is an extremely sensitive time for the Games in the wake of ticketing problems and the proposed flats demolition. With that in mind, more care than ever should be taken to be transparent and accountable about budgets and who is signing them off."
At another meeting of the 2014 strategic group, held on April 1 and chaired by the First Minister, chief financial officer of Glasgow 2014 Ian Reid said the Games were on course to be delivered within budget. However, he made a point of stating that the overall budget included the contingency fund and the separate special reserve fund, which can only be used with Mr Salmond's personal approval.
Previously, cash from the operational contingency fund has been used to extend leases on venues and to pay for rising costs of transport, logistics and venue preparation.
The most recent use of contingency fund cash, approved by the strategic group, will be to enhance the spectator experience by improving "sport presentation", which includes video boards, announcements, music, lighting, and the way athletes enter the field of play.
The general contingency budget, which originally stood at more than £70m, was revised in late 2012 after £25m was transferred to help pay for increased security costs and £4m was transferred to Glasgow City Council.
In 2010 Liz Hunter, then the Scottish Government's director of equalities, social inclusion and sport directorate, told Holyrood's Public Audit Committee it was hoped that the contingency and special reserve funds would be left untouched. The reserve fund, she said, was intended to be used only if a "really unexpected, left-field event" took place.
The overall Games budget of £563m is expected to be spent.
A Glasgow 2014 spokeswoman said: "The discussion with strategic group outlined the key financial considerations over the next 10 months which will assist in determining the Final Outturn Forecast. These factors include the financial governance arrangements of Games-time C3 (Command, Control and Communication) structures, dissolution arrangements and financial provisions for unknowns. Such provisions may be met from Glasgow 2014 contingency funds which include the Special Reserve."