The organisation's design review panel has called for a 'fundamental reconsideration' of the project off Leith Walk, which includes proposals for 400 homes, retail space and a masonic lodge.
Among the panel's main concerns is the approach to the public and private spaces - in particular the 'huge' underground car park for residents.
The report from the review meeting says: 'The quality of environment in this vast space is likely to be hostile- and the sheer scale of the proposed parking garage presents significant management and operational issues.'
The A+DS panel was also worried about the quality of the 'architectural forms' on the Shrub Place site, which features a number of listed buildings.
The report goes on: 'The proposals for the flats within the retained listed buildings are also of concern.
'The larger retained building is to have flats set back from the building line, which are to be built as independent units within the existing volume.
'On first inspection the approach appears interesting, but on further examination it raises real concerns over the quality of space and the effect on the environment within the flats.'
In response, a spokesperson for Broadway Malyan said: 'We are aware of the A+DS comments and have been working closely with all departments in Edinburgh City Council to address the outstanding issues.'
It is not the first time Shrub Place has been embroiled in controversy. Wimpey Homes Scotland spent five years working on a project for the site before deciding to walk away from the development in 2004.