McLaren are ninth of 10 teams in the constructors' championship and have directed much of the blame at Honda, whose engine has suffered embarrassing failures and is no match for rivals.
"Working with McLaren, I’ve realised that they are a very big company which is very systematic," Masashi Yamamoto said in an interview published on the Honda website (en.hondaracingf1.com).
"It’s obviously very strong because of that but at the same time they can find it hard to adapt to change."
He gave no specific examples.
Similar comments have been made in the past about Honda, who announced with McLaren last Friday that their partnership was ending.
McLaren, the sport's second most successful team in terms of race wins, will be teaming up with Renault in 2018 while Honda are joining Red Bull-owned Toro Rosso.
Yamamoto said Honda would have preferred to stay with McLaren but recognised they had not been able to reach performance and reliability targets set by the team.
The company was determined to succeed with its Formula One project, however, and still had three years with the current engine regulations to show what it could do.
Toro Rosso principal Franz Tost understood Japanese culture, said Yamamoto, and communication was good.
"We have seen that they also have a young factory and are growing, which for Honda is very important because we can work with the same mentality and have the same approach," he added.
"If we compare both teams with different cuisines, let’s say McLaren is a very sophisticated French cuisine, that’s the way it is.
"Then Toro Rosso is more like a countryside, homemade delicious stew where you can add new ingredients. We’re excited to do that."
(Reporting by Alan Baldwin, Editing by Ken Ferris)
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