كتب : Amro Hassan
Nistelrooy stormed out of the training ground before United's game against Charlton in the Premiership's last round on Sunday after he was left out of the starting line-up.
"It's straight forward, that's all we need to say at the moment, we'll be discussing it with the club's directors," United's club quoted Ferguson as saying.
Nistelrooy has been relegated to the bench for the majority of the second season as Ferguson opted to field Frenchman Luis Saha alongside Wayne Rooney.
The Dutch striker, though, kept his scoring form and found the net 21 times to finish the season as the Premiership's second top-scorer after Arsenal's Thierry Henry.
He hoped to return to a starting role against Charlton after Rooney was ruled out, but Ferguson picked 19-year-old striker Giuseppe Rossi instead.
"There have been a couple of issues during the week which concerned me in terms of the spirit at the club, and on such an important day I just felt that Ruud should be left out," Ferguson added.
English media reported on more than one occasion that Nistelrooy suffers a tensed relationship with the boss.
If this incident put an end to Nistelrooy's future with United, he would be the third star to leave Old Trafford in the recent years following David Beckham and Roy Keane because of rows with Ferguson.