In his first interview since publication of the report's summary last year, Hassan al-Thawadi, secretary general of the World Cup 2022 Committee, said Qatar was not the only bid being investigated.
The spotlight has fallen only on the Gulf country and not on Russia, which is hosting the 2018 World Cup, or the other countries with failed bids, he said.
"I can't say if there is a prejudice against Qatar but what I can say is there is a clear bias," Al-Thawadi said in the interview to be aired on Qatar-based Al-Jazeera television.
"All the reporting on Michael Garcia, the description was, the focus was on us, on Qatar, and that was inaccurate. The simple fact was the investigation was on all bidding nations, 2018 along with 2022.
"And yet nevertheless, somehow, the focus still seems to be on us and I think that, if nothing else, clearly shows there is a bias."
The Garcia Report looked into allegations of corruption in the bidding process for the World Cup to be hosted by Russia as well as the tournament being held in Qatar four years later.
Qatar's bid has been mired in controversy, facing allegations over corruption and lack of workers' rights, and this has been compounded by events surrounding the Garcia Report.
American lawyer Michael Garcia, FIFA's ethics investigator, quit his job in disgust after an "erroneous" summary of his 430-page report was published in November, which effectively cleared Qatar and Russia.
Al-Thawadi also told Al-Jazeera that Qatar could still host the tournament in the summer despite concerns over the country's climate.
Temperatures top 40 degrees Celsius in Qatar at the time when the tournament is traditionally played in June-July.
But Qatar has long argued it has the technology for the games to be played in stadiums with cooling technology.
"Since the first days of the bid we've always said a summer World Cup is feasible in Qatar, but whatever the football community decides, we will fulfill it," said Al-Thawadi.
Qatari officials are to meet with bosses of football's world governing body, FIFA, later this month in Doha to finalise a date, with many believing the tournament will instead take place in the winter.
