The concerns have arisen despite a report by George Reid, the Scottish parliament's presiding officer, which said the final budget and July finish date were unchanged for the third month in a row.
The report, which was published on Monday, said construction manager Bovis Lend Lease would shortly present a revised strategy for the towers and that cost consultant Davis Langdon & Everest would report on the state of the contingency fund next month.
Reid said: "DLE will review the remaining contingency figure in time for February's report, taking account of the prolongation on the towers and the need for acceleration measures to maintain the overall completion date."
He added: "We are now engaged in the final push towards completion by July. We are determined to enforce a 'completion culture' on everyone involved. Everything must be programme-driven."
Reid's report also gives a detailed analysis of the overall £401m budget (see "Reid's breakdown of the Holyrood budget", right). This includes money spent from the contingency fund, such as £500,000 extra spent on toilet fit-out and £600,000 on timber and linoleum flooring.
DLE will review the need for acceleration measures to maintain the completion date
George Reid, parliament presiding officer
The news of the scheme's further difficulties came as details emerged of the Audit Scotland investigation into the project as a whole.
The budget for consultancy work on the probe, whose initial results are due out in the summer, is put at around £75,000.
Gardiner & Theobald, who completed a report for Audit Scotland into the Holyrood building in 2000, beat off competition from bidders such as Ernst & Young and Cyril Sweett to win the role at the end of last year.