A GLA source said: "We would like to see 50% affordable housing on the scheme, possibly more than that."
It is understood that the mayor sees Wood Wharf as an appropriate place for such a large slice of key worker and social housing because British Waterways is a public corporation.
British Waterways responded by noting that that its masterplan had been adopted into Tower Hamlets council's planning guidance. This calls for 30% of affordable housing.
British Waterways has unveiled a longlist of nine developers to act as its partner on Wood Wharf.
They are: Amec Developments & Morley Fund Management; Argent; British Land; Canary Group & Manhattan Loft Corporation; Development Securities; Grosvenor Estates; Hammerson UK; the Miller group; and Stanhope & First Base.
A shortlist will be announced in July and the preferred bidder will be chosen in October.