But they acted in good faith and no grounds were found for disciplinary action, the scrutiny accepts. The investigation by civil service commissioner Alistair Macdonald was ordered by Scottish Executive permanent secretary John Elvidge following the Fraser report into the Holyrood project in September.
Macdonald examined the conduct of civil servants up to June 1999, when responsibility for the project was passed to the Scottish parliament.
It was initially thought that the team of Robert Gordon, John Gibbons, Alistair Brown, Barbara Doig and Bill Armstrong would be capable of managing the scheme, but the contract became increasingly complex as costs spiralled.
Questions should have been asked as to whether further expertise was required, his report finds. "One can see now they were being asked to steer the ship through the high seas when their experience was only of working on inland waterways," it adds.
The inquiry recommends improved training in business principles and financial management for senior civil servants, extending good practice on project management and greater use of external expertise.
Elvidge said that action is already in hand. "I will consider whether we need to strengthen that action," he said. "The commissioner's advice confirms our need to look forward and build on the improvements that we have already made to our procedure in the Scottish Executive."
Opposition politicians voiced disappointment at the findings. Independent MSP Margo MacDonald had expected a more analytical investigation. "It looks as though anything short of grand larceny is okay," she said.
Scottish National Party MSP Fergus Ewing described the findings as "a classic whitewash." He added: "According to the report, there is nothing wrong with civil servants covering up the truth from ministers."
The building opened last October, three years late and at a cost of £431 million, around £380 million over budget.