The scheme, which includes a 560-berth commercial marina and will 'accommodate support vessels' during the Games, was branded 'over-complicated' and 'lacking conviction' by the design watchdog.
The report said: 'We are not convinced by the fanning geometry of the site layout proposed, which seems arbitrary, and not based on any clear idea about how the marina will be used.
'For example, the idea of a green landscape island between the facilities and restaurant building seems unrelated to this site.
'We also wonder why parking is arranged away from the water, in a way that will make it more difficult to transfer equipment onto boats.'
The statement goes on: 'In addition we are concerned that a material such as timber cladding may not perform well on such a prominent and exposed site.'
Backed by the South West Regional Development Agency, the project, which includes a mix of retail and industrial units, is one of two applications recently submitted for the Weymouth waterfront site.
The other, by Royal Haskoning for the Olympic Delivery Authority, is for the new permanent slipway, and extra raceboat parking, lifting and mooring facilities.
Atkins was unavailable for comment.