Inspectors at the zoo found that while exotic animals like pandas and koalas attract stars like Nicole Kidman the other animals are being shunned.
This is causing problems not just with their popularity but with the conditions they are being kept.
According to the inspection, the £250,000 panda enclosure, which has bullet-proof glass, was excellent but other areas like the flamingo house, which had "rotting fascia boards", were in need of repair.
Other areas that were deteriorating include the viewing overhang at the big cats' enclosure.
Assessments also found two unsafe sections of the zoo that were accessible to the public – the penguin pool and a disused herbivore pen. The penguin pool is currently being refurbished at a cost of £750,000.
Zoo bosses claim to have started making the relevant changes to the zoo and should be completed by the end of the month.
The report was conducted by Edinburgh City Council as part of a review of the attraction's licence.
It concluded: "The collection is saddled with a lot of older buildings which are deteriorating and in need of maintenance or replacement. While these usually do not represent a danger to animals, staff or the public they tend to detract from the visit experience and are in danger of being neglected in favour of new exhibits."
It has been recommended the zoo has its licence renewed although it is still to be reviewed by a com-mittee later this month.