The official world rankings are used to determine who qualifies for the Olympics, but events on the breakaway LIV Golf circuit are still ineligible for points.
Several big names from the Saudi-backed tour are missing the Paris Games, most controversially reigning US Open champion Bryson DeChambeau.
Niemann played in a handful of European Tour-sanctioned tournaments earlier this year to ensure he remained as one of the leading two Chileans in the rankings to qualify.
"No," he said when asked if the qualifying system was fair.
"I don't think it's fair... Because you don't have the best players right now, I feel like."
Niemann was given exemptions to play in the Masters and the US Open earlier this year following a brilliant start to the season which delivered two LIV wins and the Australian Open title.
Victory at Le Golf National this week would give him a place at all four majors next year as well as a gold medal.
The 25-year-old started well, making five birdies and an eagle in a five-under-par first round of 66.
"If you didn't have those four majors for a win, I would have the same intensity," he said. "I will have the same motivation to win.
"I feel like this is the Olympics and (I've) got to focus more on winning medals than winning my way into the majors."
Other LIV players competing in the Olympic tournament include Spain's two-time major champion Jon Rahm and Niemann's Chile teammate Mito Pereira.
