A CABE source said it was unhappy with the shape of the building, which resembles a row of ski slopes varying in height from six to 12 storeys.
Foster changed the scheme from two buildings to one last year after residents and market stallholders expressed diquiet.
CABE chairman Sir Stuart Lipton said last week the body was looking closely at plans for the scheme, which was first proposed by developer Spitalfields Development Group 14 years ago.
The decision by CABE to intervene came as architect Piers Gough was accused of a conflict of interest by the scheme's opponents as their campaign to save the market was stepped up this week.
The Spitalfields Market Under Threat campaign believes that Gough should not be allowed to comment on the scheme in his role as a member of English Heritage's London advisory committee because his practice, CZWG, has been asked to design a scheme on a neighbouring section of the market by developer Ballymore.
A CABE source said the watchdog was unhappy with the shape of the building, which resembles a row of ski slopes
A spokesperson for SMUT, which believes that the Foster redevelopment for the Spitalfields Development Group would stifle local enterprise, said: "Quite clearly someone who is on the advisory committee should not be seen to be profiting from any development there."
But Gough defended his role. He said: "Any conflicts of interest at meetings are always revealed to the chair. If I'm a neighbouring architect, I always say so."
The architect added that when the Foster scheme was presented to the CABE review committee he sits on, he declared an interest.
Gough said the nature of the Ballymore scheme would be affected by Foster's designs.