Contractor Balfour Beatty has informed Portobello High School that it is unable to complete the project before pupils move onto the new campus in August 2016.
It is understood there is an issue securing a drainage connection with Scottish Water.
In a letter to parents, headteacher Ruth McKay said: "Work is ongoing to resolve the issue, however in the meantime we are planning on the basis that we will move into the new school in January 2017.
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"There is still a chance that this issue can be resolved more quickly and if that is the case, we would move at the earliest school holiday period which would be the October 2016 break.
"We are keen to achieve this if at all possible."
When completed, the new Portobello High School will be able to house 1,400 pupils.
Features include a swimming pool and two all-weather pitches.
Construction got underway in October 2014 after the council took a Private Bill to the Scottish Parliament, allowing the new facility to be built on Portobello Park.
(LM)
