Part of the increase was down to rising prices between plans being completed and construction taking place, the audit office said.
Auditors investigated how seven major capital projects mainly funded by the Department of Culture, Arts and Leisure - the Ulster Museum, Lyric Theatre, Metropolitan Arts Centre, Public Records Office, Crescent Arts Centre and Tollymore National Outdoor Centre - performed against time and cost targets.
On Friday, comptroller and auditor general Kieran Donnelly said: "It is disappointing that most of the construction work did not go according to plan, with delays and cost overruns which resulted in all seven projects needing additional funding."
The combined final cost of the seven projects was £103.4m, £24.8m or 31% more than the £78.6m estimated in the original business cases.
The rate of increase ranged from 3.2% for the Public Records Office to a massive 91.3% for the Metropolitan Arts Centre (MAC).
Costs for the MAC, which opened last year and has staged world-class exhibitions and theatre, rose from £9.2m to £17.6m when additional areas were added to the design.
Most projects experienced delays when compared to initial forecasts.
Changes in the business cases, the rising cost of construction and unclear objectives contributed to inflation across the projects, the audit office said.
Six of the seven projects experienced delays ranging from seven months to two and a half years.
The business case for the Lyric provided no indication of an estimated completion date.
The Assembly Committee for Culture, Arts and Leisure has expressed concern about the Northern Ireland Audit Office findings.
Michelle McIlveen, chairperson of the committee, said: "Committee members discussed the Audit Office report and Members voiced reservations about how the Department oversaw these projects.
"The Department does not appear to have made full use of the technical advice made available to it and the Audit Office has made it clear that decisions taken by the Department did not always follow a clear audit trail. This should not be the case when public money is being used," the DUP MLA added.
Nigel Smyth, director of the Confederation of British Industry in NI, said: "At a time when the Northern Ireland Executive has a much more limited capital infrastructure funding pot than in recent years, there has to be a greater handle taken on spiralling costs even when, given its wider economic impacts, infrastructure development is in itself something we strongly support."
The report noted that the firm behind the Lyric in Belfast, Gilbert Ash NI Ltd builders, made a £150,000 donation towards construction costs, which was disclosed immediately by the Lyric.
The firm bid for and won the £10.9m contract in a separate tendering process carried out by a different team from the Lyric's fundraising department.
Despite submitting the most expensive initial estimate, Gilbert Ash was given the job following adjustments because its bid was most "economically advantageous".
The audit office report said: "In the case of the Lyric Theatre project, the investment decision maker did not identify the potential for conflict of interest and no action was taken to fully consider and record events and decisions regarding the Gilbert Ash NI Ltd patronage in an open and transparent way."
The original Lyric was built in 1968, but by the 1990s was unable to handle the expanding programme of activities and breached health and safety legislation.
Its rebuild was funded by an Arts Council lottery grant, the Department for Culture, Arts and Leisure and fundraising by the Lyric itself.
Mr Donnelly said his team had been unable to obtain any assurance that the tender evaluation process had been applied in line with best practice or that perceived conflicts of interest had been managed.
His audit report noted a full and complete record of the process of weighing the various tenders was unavailable and no representative of government was present at an evaluation meeting, the latter a "major breakdown" in the assurance process surrounding public expenditure.
The audit office said the project manager of the Lyric Theatre rebuild worked with Gilbert Ash NI Ltd on the extension to the Grand Opera House from 2005 to 2007.
"The department was unable to provide assurances that potential conflicts of interest had been managed appropriately," it added.
"We would not seek to discourage philanthropy in projects such as the Lyric Theatre, however, it is essential that public bodies identify and manage the potential for any perceived conflict of interest."
A spokesperson for the Lyric said the audit dealt with the department's management of seven capital projects, including the theatre.
"The Lyric notes that the Department has accepted the recommendations made in the report," he added.
"Any further queries about the Audit Office report should be directed to the Department."
A spokesman for the MAC said the findings of the report are a matter for DCAL.
"We do however wish to point out that in the intervening years between the initial concept and the start of the actual tender process that the scale and scope of the MAC project had changed significantly.
"This resulted in, for example, 900sqm additional gallery space - allowing the MAC to be the world class facility we had envisaged.
"These changes were fully approved before the tender was issued. The final project tender issued came in on budget."
He maintained the MAC was an excellent example of local stakeholders working together to deliver a major capital project in Northern Ireland.
"The MAC has had a dramatic effect on the economic fortunes of its vicinity and has attracted more than 270,000 visitors in less than 12 months, more than 100,000 over target.
"We will continue to work together with our funders to demonstrate the value for money an award- winning venue such as the MAC offers to Northern Ireland."
Ms McIlveen added: "Estimates of both project costs and time needed for completion appear to have been well off the mark; and missing paperwork with regard to the Lyric Theatre rebuild contract has raised significant questions about whether best practice was followed."
The Assembly committee will now write to the Culture Minister Carál Ní Chuilín regarding the report's findings.