Fernandes was on Sunday in action as the Premier League season played out its final matchday ahead of the unique mid-season break to accomodate the World Cup in the Gulf state, which kicks off a week today.
Controversy has surrounded Qatar's hosting of the finals since they were awarded in 2010, with the country's treatment of migrant workers and criminalisation of same-sex relationships among the issues which have caused the most concern.
Following United's win at Craven Cottage, Fernandes was asked for his thoughts on taking a break from domestic action to play in the showpiece tournament in the Gulf state.
"The World Cup is not the ideal time to be playing it, for everyone - kids are at school, people will be working. It will not be the best for people to watch the games," Fernandes said on Sky Sports.
"We have seen the surroundings over the past few weeks and months, and about people who have died on the construction of the stadiums. We are not happy for that.
"We want football to be for everyone, and get everyone included and involved in the World Cup. It is the World Cup, it is for everyone - doesn't matter who. These kind of things I think should not happen at any time.
"But for a World Cup that is more than football - it is a party for fans and players, and a joy to watch, should be done in a better way."
Denmark midfielder Christian Eriksen was also on the scoresheet as United beat Fulham at Craven Cottage, his first goal for the club, and gave his views on Qatar 2022.
"It has been mentioned a lot," Eriksen said. "No matter where it is, it's football. We've qualified, and we're just going to play football. I totally agree with Bruno. There is a lot on focus on it, how the World Cup has happened and why it is in Qatar. Everyone agrees it hasn't been done in the right way.
"We are footballers, we play football - politics is about something above us to make that decision. Of course we try to say our thing and do what we can. We want to get focused on it, but the change has to come from somewhere else."
Additional reporting by Press Association.