McQuaid, president of the Swiss-based International Cycling Union (UCI), said he was unable to join his colleagues evaluating Tokyo, Madrid and Istanbul — the three cities bidding to host the 2020 Games — in March.
The Irishman will be replaced by Patrick Baumann, the secretary general of FIBA, the international basketball federation.
"Pat McQuaid has decided to step down from the IOC Evaluation Commission as he was unable to attend the three visits to the Candidate Cities in March," the IOC said in a statement.
"He has been replaced by FIBA Secretary General and IOC Member Patrick Baumann."
The UCI, headquartered in Aigle, a small town in the canton of Vaud, has been fighting a rearguard action in the aftermath of the Lance Armstrong scandal.
The American, who was stripped of his seven Tour de France titles and banned for life after being accused of widespread and systematic doping, last week finally confessed to using drugs to fuel his victories.
But the UCI has been accused of turning a blind eye to Armstrong's cheating during his Tour de France wins between 1999 and 2005 when the international cycling body was under the control of Dutchman Hein Verbruggen.
"Nothing was ever covered up," Verbruggen told the ANP news agency last week.
"The UCI has always fought against doping."
The cycling body has already set up a commission to look into the Armstrong affair.