Ex-MotoGP rider Bautista has kicked off his WSBK career with 11 consecutive victories, sweeping the board at each of the first four rounds of 2019 aboard the new Ducati V4 R.
Rea said after last weekend's Assen round, during which his run of second place finishes came to an end, that he could not foresee an end to his Spanish rival's dominance.
The Kawasaki rider believes that Ducati's strategy of making a specialised road bike similar to a MotoGP machine might become the norm in future seasons - and that this would be bad for the championship.
"I'm not happy about not winning, but you have to accept it, even if it's mentally hard to do it," Rea told Spanish publication Marca. "Fortunately for me I won in the last four years, but for the outside world it was predictable or boring, and I was winning by a second or two.
"These people will be happy because there's a different winner, but it's a disaster for the championship because they wanted to change things."
He added: "The [V4] bike has an incredible level. Their own marketing strategy says 'it's a MotoGP bike'. Ducati said it when they presented the bike.
"Congratulations to them, but this championship is about balancing things, to help privateer teams be competitive. I'm worried about the future if Honda, Yamaha and Kawasaki do the same thing with €40,000 road bikes."
Asked if he was worried about being seen to be whining, Rea replied: "I'm not always complaining, I'm just talking about reality. If you talk to other riders they have the same opinion.
"At Phillip Island I said that the Ducati had a big advantage and the comments were that I was complaining, but it's people who are very happy to see I'm not winning.
"In Spain, some fans said 'Jonny, you are the best, keep pushing'. That's very nice.
"We have to keep working. There are circuits that are favourable for me coming up. Of course I won't dominate like in the past, but I'll be closer."
Jonathan Rea, Kawasaki Racing, Alvaro Bautista, Aruba.it Racing-Ducati Team, Michael van der Mark, Pata Yamaha
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