Robert Black made his comments in a report on the scheme that was submitted to MSPs this week. He said: "Completion of the Holyrood project is a moving target. Even at this advanced stage of construction further cost increases and slippage cannot be ruled out."
Black, who was assisted by QS Gardiner & Theobald on the Audit Scotland report, said the uncertainty about cost and completion would probably prompt Audit Scotland to produce a third report.
Building reported in May that the final budget for the scheme, which is due to be finished in September, was likely to rise to £450m. This was strenuously denied by parliamentary officials.
The report laid the blame for the 20-month delay and £400m increase in the budget on the number of design variations and the late supply of information. It added that there was no single point of leadership or control.
The report criticised the project management saying: "For this project, design development became a process of costing a developing design rather than developing the design within a cost limit."
The report analyses 20 of the specialist packages on the construction management deal. It found that 13 of them had fewer than three bidders, which it described as an "unusually low number for contracts of this size".
Completion of the Holyrood project is a moving target
Audit Scotland report
The auditor-general said there was "significant uncertainty" in 11 of the 20 contracts. He said design responsibility was extended to trade contractors themselves.
The total claims by the contractor for prolongation because of disruption and delay added £86m to the scheme's budget.
Black said construction management had not been used as a procurement method for a public sector scheme in Scotland before, and concluded that not enough expertise or experience was shown in the early stages of the project.