The FA are looking over the documentation from the deal, along with a number of other transfers, as they try to uncover any corruption within the game.
United have insisted that they have done nothing wrong during the signing of Howard from New York/New Jersey MetroStars.
"All our transfer deals are approved by the board of the Manchester United plc and are conducted in accordance with the Fifa and FA rules," said a club statement.
"Details of all payments involved in those deals are sent to the football authorities as required under the regulations."
The apparent payment to agents for their part in transfers seems to be the major talking point in the FA's investigations.
Sir Alex Ferguson has previously been warned by the club about using his son Jason's agency for transfer dealings - but Ferguson Jr has insisted he had no part in the Howard deal.
"We were not involved in the transfer of Tim Howard," insisted Jason Ferguson.
