In other documents filed with the Brooklyn court, Donaghy's lawyers responded to the NBA's claim that he must pay $1 million in restitution to cover the cost of the league's private investigation.
The letter alleging referees altered games mentions only the year 2005, but the circumstances make it apparent that it is referring to the Rockets-Mavs series.
"Team 3 lost the first two games in the series and Team 3's owner complained to NBA officials," the letter said. "Team 3's owner alleged that referees were letting a Team 4 player get away with illegal screens. NBA Executive Y told Referee Supervisor Z that the referees for that game were to enforce the screening rules strictly against that Team 4 player. Referee Supervisor Z informed the referees about his instructions. As an alternate referee for that game, Tim also received these instructions."
Mavs owner Mark Cuban complained after his team lost the first two games of the series, and Dallas went on to beat Houston in seven games. Van Gundy said that a working referee had told him about the league's plan. Donaghy's letter claims that Supervisor Z contacted the coach. Van Gundy was fined $100,000.
Looking at box scores from the series, however, the only game in which Yao fouled out was Game 1. He did average 4.4 fouls per game in the series.
The letter also details an incident in the 2002 playoffs in which Donaghy alleges that two referees, who were known as NBA "company men," wanted to extend a series to seven games. "Team 5" could have wrapped up the series in Game 6 but saw two players foul out, lost the game and ultimately the series.
Only one series went to seven games in the 2002 playoffs: Los Angeles Lakers against Sacramento Kings.
In Game 6, the Lakers made 34-of-40 free throws to 18-of-25 for the Kings. In the fourth quarter alone, Los Angeles hit 21-of-27 from the line while Sacramento made 7-of-9. After that game, a 106-102 Lakers win, Kings coach Rick Adelman expressed his frustration with the officiating.
"Our big guys get 20 fouls tonight and [Shaquille O'Neal] gets four? You tell me how the game went," Adelman said. "It's just the way it is. Obviously, they got the game called the way they wanted to get it called."
The Lakers went on to win the championship in 2002.
Donaghy also alleges that team executives conspired with the league to prevent star players from being called for too many fouls or being ejected. He claimed that league officials told referees that doing so would "hurt ticket sales and television ratings."
According to the letter, when an official did eject a star player in the first quarter of a game in 2000, he was privately reprimanded.
In addition to game-altering allegations, Donaghy's letter claims that many officials carry on "relationships" with team executives, coaches and players that violate their NBA contracts.
"Tim described one referee's use of a team's practice facility to exercise and another's frequent tennis matches with a team's coach," the letter said.
The NBA issued a statement on Tuesday from Richard Buchanan, NBA executive vice president and general counsel.
"According to Mr. Donaghy, all of his allegations have previously been made to the FBI and the U.S. Attorney, and they are clearly being disclosed now as part of his desperate attempt to lighten the sentence that will be imposed for his criminal conduct," the statement read. "The NBA remains vigilant in protecting the integrity of our game and has fully cooperated with the government at every stage of its investigation. The only criminal activity uncovered is Mr. Donaghy's."
Lamell McMorris, head of the NBA referees union, also issued a statement:
"Tim Donaghy has had honesty and credibility issues from the get-go," the statement read. "He is a convicted felon who has not yet been sentenced for the criminal conduct he has already admitted to. He may be willing to say anything to help his cause and he may believe these most recent allegations will help his agenda. I'm not aware of any improper conduct by any current NBA referee in the playoffs six years ago or any conspiracy by the NBA to affect the outcome of any game then or now. Frankly we're tired of Tim Donaghy's cat and mouse games."
Donaghy's attorney and federal prosecutors declined to comment to The Associated Press on Tuesday. Donaghy faces up to 33 months in prison.
Information from The Associated Press was used in this report.