About 80% of Scottish council building projects have been delayed and 60% have gone over budget, the public spending watchdog has found.

One project ran more than four years behind schedule while another was nearly three times the original cost estimate.

The average delay was 17 months and the total cost was 26% higher than the initial combined estimate, an overspend of £89 million, according to an Accounts Commission report.

Combined council debt has increased by 40% in the past five years and could rise further in the years to come, the commission also warned.

However, the report cannot identify the full scale of the problem due to "significant gaps" in information provided.

One-fifth of councils did not provide initial cost estimates and one-third did not provide early timescale projections, either because they were not done or the records were lost.

Most early cost and timescale estimates proved to be inaccurate, business case development was largely weak and information monitoring insufficient, according to the commission.

It has called for strong leadership in the coming years, with money for capital investment expected to fall significantly until 2014/15 and beyond.

The review stated: "A total of 78% of projects took at least two months longer to complete than estimated at initial approval, with only 19% completed on time.

"The average delay was 17 months, with delays ranging from three months to 52 months."

The report does not say which project took 52 months.

The Edinburgh International Conference Centre has been delayed by 43 months, largely due to the withdrawal of the original contractor, but it has come in 25% under budget at £84.6m.

The report stated: "Of the 35 (traditionally financed) projects where final costs were known, the majority had initial cost estimates that proved to be significant under-estimates.

"Councils completed 13 projects, costing £355m, on or within the initial cost estimate. One project had final costs that exceeded the initial cost estimate by 1%.

"Twenty-one projects had final costs that were significantly higher – between 5% and 189% – than the initial cost estimate.

"These projects had a combined outturn cost of £344m, £89m (26%) more than their combined initial cost estimates."

The report does not say which project ran 189% over budget.

The cost of the Dunfermline flood prevention scheme rose by 152%, from £9.8m to £24.7m, and has been delayed by two years due to design problems and a conflict between the council and contractor.

Total council capital spending doubled in the first decade of the millennium from £1.2 billion in 2000/01 to nearly £2.4bn in 2008/09, a position it returned to last year following a dip during the recession.

The report said: "Councils' combined debt levels have increased by 39% from £9.3bn in 2007/08 to £12.9bn in 2011/12.

"With further borrowing and private finance investment planned over the next few years, overall debt levels may continue to rise."

It added: "There are some significant gaps in the availability of cost and time information.

"For one in five projects, the relevant council could not provide a cost estimate at the initial approval stage, either because project costs were not estimated at this time or data were unavailable.

"Similarly, 20 out of 63 (32%) could not provide a time estimate at the initial approval stage.

"Without detailed, accurate and realistic business cases, particularly at the initial approval stage, key performance information on aims, cost, time, scope and risk may not be clearly defined.

"This could make it more difficult to hold decision-makers to account if problems arise later in the project."