Under the terms of the joint venture deal with the Lend Lease-led Meridian Delta consortium, the government will receive cash equal to the value of the land as the developments are sold, as well as half the profit.
The government said last month that it hoped to recoup £500m of the £600m it has spent on the site, but it is thought that this calculation was based on the assumption that 30% of the site would be set aside for affordable homes, in line with Greenwich council's planning regulations.
Livingstone has since said that he wants to raise that figure to 50%, most of which would be pencilled in for social housing – which is particularly costly because of recent falls in subsidies for them.
The Meridian Delta consortium said it was not possible to quantify the impact of the affordable housing quota. In a statement, the consortium said: "MDL has not put a figure on this because there are so many variables and significant costs associated with developing on the peninsula."
A consortium source did concede that MDL would be affected, but believed it could reduce the impact after talks.