A meeting on Friday overruled the planners' recommendation to approve the architect's proposals - that would have included a 40-storey tower - on four major counts.
The councillors complained about the 'siting, layout, height and visibility' of the scheme, and claimed it failed to relate satisfactorily to the existing marina development and was out of keeping with nearby conservation areas.
A council spokesperson also panned the project for its 'size, height and bulk' which, they said, 'represented an overdevelopment'.
The council also claimed that within the scheme there would be 'insufficient scope for public and private amenity space', and that the development would generate 'a significant volume of traffic and parking problems.'
The sub-committee, which was chaired by Councillor Les Hamilton, voted down the plans nine to three.
The practice's proposals included: 988 flats, 40 per cent of which will be affordable units; 504m 2of harbour control and marina offices; a community centre and visitor viewing gallery and 176 car parking spaces, along with a lifeboat station.
A spokesperson for Wilkinson Eyre said: 'Despite having the backing of local authority planning officers, our scheme to redevelop Brighton Marina on behalf of Brunswick Developments did not receive planning permission last week.
'We are disappointed by the decision but optimistic that the situation will be resolved.'