Having stoked the flames of controversy last week by suggesting it had been a desperate measure from Manchester United to bring Paul Scholes out of retirement in January, Vieira seemed to suggest United were benefiting from refereeing decisions in a pre-arranged interview with the BBC's Dan Roan.
He said: "I am very angry with Dan Roan. I feel he has misrepresented me."
Vieira's comments emerged in the wake of Fulham's 1-0 defeat at Old Trafford on Monday, when the Cottagers were denied a last-minute penalty when Michael Carrick barged Danny Murphy inside the box.
Under the circumstances, the comments were inflammatory and appeared oddly timed given City have now fallen three points behind in their attempt to win the championship.
Although they have not denied Vieira made the comments that have been reported, City have released a strongly-worded statement condemning the manner in which they were used during an interview which was supposed to be part of Vieira's charity work for Football Against Hunger, a campaign to tackle starvation in Africa.
"Patrick Vieira has expressed his disappointment and anger at what he feels is a serious and cynical misrepresentation of an interview he gave to the BBC," said the statement.
"Manchester City's Football Development Executive gave the interview at the annual SoccerEx exhibition at the GMEX Convention Centre on Wednesday afternoon. He was representing Football Against Hunger, a campaign to tackle starvation in Africa.
"An interview given to the BBC's Dan Roan contained what Patrick feels was a very leading line of questions regarding Manchester United supposedly receiving favourable treatment by referees. Patrick feels that his views have been deliberately taken out of context."
Vieira said: "I made it clear in the interview twice that I wanted to avoid criticising United and even stated that I didn't watch the United game against Fulham and had not seen the incident to which the reporter referred. That part of the interview was ignored and my comments were taken completely out of context."
Source: PA
Source: PA