An investigation by the National Audit Office concluded that, although problems were discovered in the New Millennium Experience Company's procurement activities, there was no proof of "systematic fraud".
The report, called Winding-up the New Millennium Experience Company, studied allegations that emerged in 2000 about contracts signed by the firm with dome suppliers, including contractors.
Scotland Yard launched two investigations into the NMEC in September 2000 after anomalies were discovered by dome auditor Pricewaterhouse Coopers, one of which was thought to centre on a maintenance contract.
The report, published on Wednesday, said: "There was no evidence of systematic fraud or any additional cases of suspected fraud where the weight of evidence would justify further investigation."
However, the NMEC's procurement activities did come in for criticism. The NAO found that the firm lacked basic controls such as invoice authorisation or legally binding relationships with suppliers.
The report said: "[Pricewaterhouse Coopers] identified 129 suppliers, each of which between 1998 and 2000 had rendered invoices totalling £50,000 or more, for which they could not find either a contract or a single tender action form."
The report also includes the findings of contractor Bovis Lend Lease and consultant Capita. Both firms said the NMEC's processes improved after January 2001. Bovis monitored the decommissioning of the site between January and December 2001 and found the total cost of £12.4m was value for money.
Capita found that since January 2001, the NMEC had controlled its finance properly.
The NAO said the project was a lesson for those managing high-profile projects. It said: "This report highlights the importance of proper records and internal controls, and a clear focus on public accountability."
The site is set to be taken over by Meridian Delta, a consortium that includes Bovis' owner Lend Lease. It plans to turn the site into a housing and leisure complex.