The accounts also show that the agent Pini Zahavi received £1.8m from the club in the year for both buying and selling players.
He was paid the majority of his fee in the Rio Ferdinand deal, £825,000; for his part in Louis Saha's move from Fulham he got around £500,000 and there was even £500,000 for offloading Juan Veron to Chelsea.
"If we didn't think it was worth it as a board we wouldn't have spent it," said Gill commenting on the sale of Veron. The chief executive is comfortable about explaining the deal to shareholders if he has to. He said today: "We will meet with the representatives of Magnier and McManus now the results are out and similarly with the Glazer partnership. Our relationship with both major shareholders is good."
Finance director Nick Humby announced there would be changes after conducting a review of United's transfer dealings in May in the wake of the 99 questions.
In an effort to remove any suspicions of wrongdoing, United also announced the club would not use Elite Sports, the Manchester based agency in which Sir Alex Ferguson's son Jason was a director.
They also introduced improved record-keeping, new rules on appointing agents and stricter limits on how much they would be paid.
Since then a £250,000 instalment has been paid to agent Alex Black for his part in Alan Smith's move from Leeds. There has also been a deal sealed to pay Paul Stretford's Proactive Sports Management up to £1.5m for helping negotiate Wayne Rooney's transfer from Everton, although that happened after the period covered by today's accounts.