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Figures comparing the performance of Scottish councils also showed the Capital had the lowest satisfaction level with schools out of all 32 authorities.
Opposition councillors described the figures as a “wake-up call”.
The statistics showed Edinburgh’s spending on primary schools in 2016/17 was £4105 per pupil compared with a Scottish average of £4788. Only East Lothian spent less.
In secondary schools, Edinburgh spent £6252 per pupil against an average of £6806 - again the second lowest.
And on pre-school education the Capital spent £2911 per pupil compared with an average of £4246 - the third lowest, with West Lothian in second place.
The figures, from the Local Government Benchmarking Framework, showed satisfaction with the city’s schools was just 62.7 per cent where the average is 75.3 per cent.
It is understood the survey may have been carried out around the time when 17 city schools, built or refurbished under a public private partnership agreement, had to close for urgent structural repairs.
The council also believes the efficient use of buildings and the lack of rural locations within the authority help to explain the lower spending.
Tory education spokesman Callum Laidlaw said the findings were “extremely disappointing”.
And he linked the dissatisfaction to the poor condition of some school buildings, as well as the controversy over the plans to merge Currie High and the Wester Hailes Education Centre.
He said: “It reflects the issues we have had both with the school estate and the uncertainty around the future of some of our schools.
“Our teachers are doing an excellent job. A lot of the dissatisfaction I come across is not to do with teaching quality or standards, but about the fabric and the facilities. If you look at schools like Trinity or Liberton, it’s obvious.
“The council should be doing more, but the Scottish Government needs to recognise we have significant pressures on the fabric of our schools and make sure the funding Edinburgh gets takes that into account.”
Green education spokeswoman Cllr Mary Campbell said: “This is a real wake-up call for the council on how our schools are doing and how that is viewed by the city.
“And it is a wake-up call for Scottish Government in how it can better fund the capital and back the fantastic work that our school staff and families are doing. From well-documented problems with some school buildings to basic shortages in materials, support staff and teachers, the stark reality is that Edinburgh needs to invest more in education.”
The Lib Dems called for an action plan Education spokeswoman Louise Young said: “Parents and pupils deserve much better than this. Education and improving the standards in our schools needs to be at the very top of this council’s priorities.
“Yet these latest figures show the administration is simply failing to meet a series of its own performance targets. Parent satisfaction scores are alarmingly low.”
Other findings included a lower-than-average 92.5 per cent of Edinburgh pupils going on to work, further education or training when they leave school against the Scottish-wide figure of 93.7 per cent.
The council pointed out the satisfaction figures quoted came from a survey of adults in general rather than parents of children at school. However, this would also apply to all the other local authorities.
Council leader Adam McVey said: “It’s worth noting 83 per cent said they were satisfied with our local schools in our most recent survey of parents.
“We would also expect that our planned programme of investment in our school estate, including the additional £20m invested in our schools this summer, will improve satisfaction and performance in future years.
“Our central focus is on improving the opportunities for young people across the city and this year’s exam results in council-run schools demonstrate the strong performance of students, particularly in S5 and S6, with the pass rate in highers up three per cent from last year.”
And on the issue of spending figures, the council argued fuller schools meant lower costs per pupil. Education convener Ian Perry said: “Our school rolls are rising, with many schools operating at capacity, which means we can achieve maximum efficiency and a lower cost per pupil. Factors that can increase the cost per pupil include low capacity levels or location in rural areas, thus increasing the cost of transport, and this is not the case in Edinburgh.”