In a meeting last Thursday, the council's major planning applications committee said it is unlikely to give planning permission to the scheme unless the architect scales down the height and bulk of the building.
Acting on recommendations from the council's planning officers, the committee called for a height restriction of 20 m on the redevelopment of Egton House, a key building in the scheme.
The architect had envisaged increasing Egton House from five to eight storeys, but Westminster has asked for the removal of these additional floors. Local groups had complained that the architect's proposal would obscure views of the historic All Souls Church, which stands next to the site.
The committee also objected to the proposed heights of the scheme's three service towers, and was particularly critical of their effect on the strategic view of the Palace of Westminster.
The committee added that a bridge linking buildings in the scheme was poorly designed. The draft minutes of the meeting, said: "A more visually interesting, innovative design treatment is considered necessary."
A more visually interesting, innovative design is necessary
Westminster council report
Carl Powell, director of planning and transportation at Westminster, insisted that the council was largely in favour of the scheme, but that further discussions with the BBC were now important.
The BBC, although understood to be stung by the blow, said MacCormac Jamieson Prichard was addressing the issues raised and hopes to submit its final designs for the scheme in June.
Although the scheme has received strong letters of support from architecture watchdog CABE, English Heritage has objected to it on the grounds that part-demolition of the existing site will be required.
EH historic buildings inspector Steven Robb said: "Our main concern is that Broadcasting House is a grade II*-listed building in a conservation area."
Earlier this month the BBC invited construction managers to apply to oversee the scheme. However, there is concern among construction managers that if the BBC decides to allow its property partner Land Securities Trillium to make the appointment, Bovis Lend Lease will win the contract because of its close relationship with the property firm.