The Malaysian, who also owns English second tier football club Queens Park Rangers, said Formula One needed to act so the performance gap between teams could be reduced and all could have a chance.
Caterham finished last overall in 2013 and have yet to score a point in four seasons that have seen Red Bull and Germany's Sebastian Vettel rack up four successive championships.
The sport has made a controversial rule change to award double points, 50 for the winner instead of the usual 25, for the last race in Abu Dhabi in a bid to keep the title outcome open right to the end.
Despite overwhelming opposition from fans on social media, and Vettel describing the move as 'absurd', teams appear unlikely to overturn it.
"The double points is a fake fix," Fernandes told reporters at a media event at the Caterham factory in central England. "What's better is to solve the issue and make the racing more compact.
"So that Sauber...or a Force India could make an upset. That's what people like to see, that's what people come to watch and that's what's missing in Formula One," he added.
"We spend all this money and time on engines, KERS whatever. But the gap between the haves and have-nots has made racing boring."
Fernandes, who has spoken out previously about the need for a cost cap that the governing FIA wants to introduce in 2015, said something had to be done to reduce expenditure and increase excitement.
"Football's way ahead, with the financial fair play," he declared. "Look at this transfer window. There's not that much craziness going around."
The Malaysian, who also runs the AirAsia budget airline, said Formula One teams were struggling and the sport needed to "get its act together" regardless of who was in charge.
"Everyone's just worried about whether they can be two tenths of a second faster than others and everyone is trying to screw each other. And now we are all in a mess. Because you can't have Formula One with four teams.
"I haven't seen a consensus on anything in my four years," he added. "Formula One needs to change its financial structure."
Fernandes said the legal problems surrounding Formula One's commercial supremo Bernie Ecclestone, with an impending bribery trial in Germany seeing the 83-year-old step down from the board, could be a catalyst for change.
However, he refused to pin any blame on the Briton.
"If you want to get your house in order...that starts with the teams," said Fernandes.
"American sports run themselves much better than we do in Europe and there are lots of great models there...you generally see American sports teams increasing in value."
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
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