Council chiefs said they will “will not be left footing the bill” for the defects which have led to disruption for thousands of pupils.
The enquiry is scheduled to start this autumn when repair work is expected to be completed.
A council report confirmed the problems concerned missing wall ties.
The report stated: “Early indications are that this remains a construction quality matter as opposed to one relating to a design defect or the operating model employed.”
Construction of the schools was completed in 2005 under a £360m private finance deal with the Edinburgh Schools Partnership
The first phase of the deal saw building of 13 schools overseen by a 50/50 joint venture of Miller Construction and Amey. The second phase was built by Miller which is now owned by Galliford Try.
Council leader Andrew Burns said: “It is important that we have an independent chair for this inquiry; one who commands respect within the construction industry.
“The terms of reference will be thorough and we want the report to get to the heart of this issue and see what lessons can be learnt, not just here in Edinburgh, but across Scotland.
“When the issue came to light, our first priority was safety of pupils and staff, the second was getting pupils back into education, the third is getting the schools reopened and it is not until this has happened that the inquiry will begin.”