The overseer of public spending examined the information and communication technology (ICT) programmes, which were delayed, cancelled or hit by rising costs.
Auditor General for Scotland Caroline Gardner said the report revealed significant weaknesses in how they were planned, managed and overseen.
The projects examined involved the Crown Office and Procurator Fiscal Service (COPFS), Registers of Scotland – the body responsible for compiling and maintaining registers relating to property and other legal documents – and Disclosure Scotland, which provides information about the criminal record of those applying for certain jobs.
A total of £133.3m has been spent on the three projects so far, but Audit Scotland said the business cases for these were of variable quality.
The watchdog also highlighted "weaknesses in financial control and progress reporting", claiming "risk management was inadequate" and the findings of independent reviews were "not always acted on".
Audit Scotland went on to state there was a "failure to appreciate the complexity of the programmes" and that the organisations concerned did not have sufficient specialist knowledge.
The report said: "A key factor in the failure to deliver the programmes as intended was the public sector bodies' lack of specialist skills and experience.
"This contributed to a lack of understanding about the complexity of the programmes and an over-reliance on the supplier for key decisions affecting the design and implementation of the necessary technology." It added that the Scottish Government was "unable to provide the three public bodies with all the advice and support they sought".
Registers of Scotland paid out £112m after it reached an agreement with BT in 2004 for ongoing ICT provision and work to update its IT systems, even though the original cost was estimated to be £66m. It has now given notice to terminate the contract 20 months early.
Disclosure Scotland has spent £19 million on its Protecting Vulnerable Groups programme, which included a new ICT system to check and issue disclosure certificates.
However, the report said the programme experienced a number of significant problems when it was first introduced and is now expected to be delivered 18 months later than planned.
Meanwhile, COPFS spent £2.3m on a new programme to improve its case management system. This was expected to cost £10m in total, but the project was cancelled in November 2010 because of increased costs and a reduction in the organisation's capital budget.
Ms Gardner stressed the importance of ICT, describing it as "an important way of helping public bodies work more efficiently and deliver better and more joined-up services".
She added: "Scotland's public bodies invest heavily in ICT, spending about £740m a year, and there are several major programmes under way across the public sector."
She continued: "We examined three programmes – which have cost more than £130m in total so far – that were delayed or cancelled in order to learn lessons for other public-sector projects.
"We found significant weaknesses in how they were planned, managed and overseen. Some of this arose from a lack of specialist skills, but there were also flaws in areas of basic project management that apply to capital works of all types."
A Scottish Government spokesman said of the three ICT projects: "We have already acted on lessons learned from each of these programmes."
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