Bob Kiley, London mayor Ken Livingstone's transport commissioner, recommended the changes.
A source close to the negotiations said the changes had already been discussed. The source said: "They've already been raised in talks this year with Bob Kiley and LU. So there are no surprises."
A spokesperson for Metronet, one of the consortiums, said: "We have the modified contracts and are looking at them. We want to turn them into the final deal as soon as possible."
He added that the consortiums had about two weeks to reply to the government but that there would be no delay. The deals are expected to be finalised by the end of the year.
Transport secretary Stephen Byers said: "These proposed changes are important because they demonstrate in the clearest terms that safety will not be compromised."