The seven-time champion was fifth quickest, with team-mate George Russell fourth, both just under 0.5 seconds behind Max Verstappen of Red Bull.
The times were set in the first session, while the second was rendered irrelevant by wet conditions.
Hamilton said: “It was a really good session, the best the car has felt this year.”
Mercedes expected to struggle at Suzuka because its demanding, high-speed layout layout should expose the car’s limitations in high-speed corners.
Mercedes have been struggling to understand why the car produces less downforce on track than their simulations suggest it should.
Hamilton said: “It felt really positive. I was excited, because this is a circuit every driver loves to drive and the last couple of years we’ve had a really difficult car and balance to drive here.
“And given the difficult last few races we’ve had, great work has been done and we seem to have hit the ground in a sweeter spot so I haven’t really made any changes.”
