Ismail Bhamjee, a Fifa executive committee member, was recorded claiming that he believed Morocco had won more votes than South Africa, but Fifa manipulated the results of the secret ballot.
Questions over the bidding process for the 2010 tournament centre on a US$10 million payment by the South African government said to have been for a project to support the African diaspora in the Caribbean. The money was sent from Fifa to an account controlled by its disgraced former vice-president Jack Warner, following a request to Fifa secretary-general Jerome Valcke, from the South African Football Association.
Last week Fifa insisted neither Valcke nor any other of its senior figures were "involved in the initiation, approval and implementation" of the deal.
In the email, dated December 7, 2007, Valcke appears to be chasing a South African minister over the payment. "I have never received confirmation but more important I would like to know when the transfer can be done," he wrote.
He reminded the recipient that the plan was: "Based on a discussion between Fifa and the South African Government and also between our president and ... President Mbeki."
The message refers to an earlier letter, dated September 19, 2007, in which Valcke details the South Africans' commitment to paying US$10 million to a legacy programme for Africans in the diaspora, "specifically for the Caribbean countries".
But a spokesman for Fifa insisted the messages did not prove that Valcke and Blatter were involved.
"It is simply referring to an update given by the then president of South Africa to the Fifa president about the South African Government's formal request," she said. "That constitutes information, not involvement. As previously stated and confirmed by the South African authorities, this programme was initiated by the South African Government for the Caribbean and it was publicly announced by them at the time."
The FBI - which is investigating alleged corruption by a string of Fifa officials and issued warrants for the arrest of Warner and eight others - alleged the payment constituted a bribe in exchange for his support for the South African bid, and that Warner took much of the money for his own use.
South Africa's government has confirmed it authorised the payment but rejected suggestions it was a bribe.