Hamilton, who has not placed higher than seventh this year and did not finish in Australia a fortnight ago because of engine failure, will leave Mercedes for Ferrari at the end of the season.
He said he struggled with his tyres and steering at Suzuka, where triple world champion Max Verstappen dominated for his third win in four races.
“I did my best but the result wasn’t a good one,” said Hamilton.
“Unfortunately, that is where our car is at the moment.”
Hamilton let Mercedes team-mate George Russell pass him as he struggled with his steering.
Russell finished seventh, edging out McLaren’s Oscar Piastri late in the race.
Hamilton was one place further back and he said the team could not have expected much better.
“We need to keep working hard as today — our pace was only likely good enough for P6,” he said.
“If we want to move up the grid, then we will need to add more performance to the car.”
Mercedes boss Toto Wolff was not scheduled to attend the race in Japan but he changed his plans after his team’s poor start to the season.
Wolff refused to be disheartened by another dismal result and turned his attention towards the Chinese Grand Prix in two weeks’ time.
“Overall, this weekend has been better than the final results suggest,” said Wolff.
“We have lots to learn and there is no track-relevant excuse we will use — we need to be quicker at all circuits.
“But from what we’ve seen here, we can say that the car is becoming quicker.”
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