The Daily Mail says it is believed Ferguson was angry at Vidic's decision to play for Serbia in a Euro 2012 qualifier against Slovenia this month, even though he had been out of action for United with a calf injury for almost two months.
Vidic, 30, did not help his cause by being sent off on his return to action in last Tuesday's Champions League victory over Romanian side Otelul Galati in Bucharest.
But Ferguson was said to be particularly unhappy over his appearance for Serbia, and Vidic hinted at a disagreement when announcing his international retirement.
"The basic reason is that my commitment for the national team has been criticised by the media and therefore by the public as well for some time," said Vidic, who won 56 caps.
"I've been under fire although I turned up to play for Serbia even when I was injured and sometimes against the advice of my club."