Three-times Tour champion Contador, provisionally suspended after failing a dope test during the 2010 race, will probably be out of shape or not even cleared to participate in the world's greatest cycling race, McQuaid told Reuters.
"It is not a good place to be for Contador at the moment," McQuaid said in a telephone interview.
"We could assume that it's a possibility that he will not be at the Tour de France."
Spaniard Contador's case is in the hands of the Spanish federation (RFEC), whose ruling on the matter is not expected before the end of the month.
The RFEC has requested the UCI's expertise on the case and the sport's governing body is trying its best to get back to the Spanish federation "by the end of the month", McQuaid said.
The RFEC's decision, however, is very likely to be appealed before the Court of Arbitration for Sport (CAS) by either Contador, should he be handed a suspension, or by the UCI or the World Anti-Doping Agency (WADA) if the Spaniards were to clear the five-times grand Tour champion.
A ruling before the start of the Tour in July is not guaranteed under these circumstances.
"It is possibly correct that this is what will happen," McQuaid said.
While suspended, Contador, who has threatened to quit should he be punished, cannot take part in any competitive race and the possible appeal process before CAS is likely to take months, dramatically hampering the rider's preparations for the Tour.
He has repeatedly protested his innocence, blaming contaminated meat for the traces of banned stimulant clenbuterol found in his urine sample.
Exciting season
McQuaid is not worried for the sport and believes the 2011 season will be exciting, even without Contador and seven-times Tour champion Lance Armstrong.
Armstrong will take part in the Tour Down Under this month, but the week-long event is expected to be his last international competitive appearance.
The Armstrong vs Contador rivalry was a hot topic in the 2009 Tour, and both riders were the top attractions in this year's race even if the American quickly lost all hope of winning an unprecedented eighth title.
The Irishman is confident that Armstrong, even if the Texan is at the centre of a U.S. federal investigation into alleged doping, will be a presence "in the media".
Armstrong, who has faced doping allegations throughout his career, but never tested positive, has repeatedly denied any wrongdoing.
McQuaid also believes Contador's possible absence will create fierce competition between his rivals.
"I am confident that it will be an exciting season," McQuaid said.
"There are a lot of guys ready to fill his shoes, well, if not his shoes, the top places. It will be interesting to see the battle for the top spots.
"There are many highly motivated riders," he added, referring to 2009 world champion Cadel Evans, who is still looking to win his first grand Tour.
"Several other guys will be looking to move up. In every sport some big stars have left and the sport has not suffered from it."