McQuaid's position as UCI president has been under scrutiny following the Lance Armstrong scandal, with an independent commission set up to establish the relationship between cycling's world governing body and the Texan, who has admitted using performance-enhancing drugs in all seven of his Tour de France wins, from 1999 to 2005.
Now McQuaid has been replaced on the committee by Patrick Baumann, secretary general of basketball's world governing body.
An IOC spokesperson said in an emailed statement to Press Association Sport: "Pat McQuaid decided to step down from the IOC evaluation commission as he was unable to attend the three visits to the candidate cities in March.
"He has been replaced by FIBA secretary general and IOC member Patrick Baumann."
The election of the host city will take place on September 7, 2013, at the 125th IOC Session in Buenos Aires, Argentina.