Honda technical manager Takeo Yokoyama says HRC is having to try "more than expected" to get the 2020 RC213V to work with the new Michelin MotoGP rear tyre construction.
Michelin introduced a new rear tyre carcass for the 2020 season which offers better grip and durability in race situations.
But it has had a profound effect on the pecking order this year, with a number of riders - most notably Andrea Dovizioso on the Ducati and those on the 2020 Honda - struggling to adapt their riding to the tyre.
The 2020 Honda has proven to be a difficult motorcycle, and the added grip from the rear tyre coupled with an inertia problem surrounding the engine is causing problems under braking for its riders.
Alex Marquez, Stefan Bradl and LCR's Cal Crutchlow have also struggled to extract the maximum from the tyre in qualifying.
Speaking during the Catalan Grand Prix weekend about where the Honda needs to improve, Yokoyama said: "I think what we are working on the most is how to use the maximum potential from the new rear tyre construction.
"Honestly speaking, I don't think we are using the maximum [from the tyre] because there are some areas we had to change a lot the bike.
"The philosophy of the Honda from the tradition... we have to try a lot of things, actually a lot more than we expected when they decided to change the tyre. We are trying a lot of things.
"I wouldn't necessarily agree [the Honda deflects the tyre more], but the way to use - including the riding line - maybe needs to be changed."
As part of cost-saving measures in light of the COVID-19 pandemic, all non-concession manufacturers have had their engines frozen until the end of 2021 and will be unable to develop them.
This will force Honda to work exclusively on chassis and suspension to improve the difficult handling characteristics of the RC213V, though Yokoyama is unsure whether this will be beneficial or not to HRC.
"Of course, if we have the freedom to keep developing the engine, this is one more extra freedom to play with - not only for the horsepower, but the handling, rideability and everything," he added.
"So, when engine development is frozen, it's more complicated.
"It's more difficult to fix the problem if you have some problems on the bike, which we do have.
"If somebody asks me if it's a handicap or an advantage for Honda, I can't really judge.
"The reality is we can't change the engine, but we still have many things around it to improve the performance."