Hamilton had a time of 1 minute, 28.691 seconds, 0.446 seconds ahead of teammate Valtteri Bottas. Red Bull’s Daniel Ricciardo was third.
Ferrari drivers Kimi Raikkonen and Sebastian Vettel rounded out the top five in the Friday practice.
With five races to go, Hamilton would move a step closer to a winning a fifth world championship with a win in Suzuka.
Hamilton has won five of the last six Formula One races and three of the last four at the Japanese Grand Prix.
After winning the Russian GP last week, Hamilton leads Vettel by 50 points. Even if Vettel wins all five remaining races, he’s not guaranteed to beat Hamilton.
Conditions were cloudy at Suzuka with rain forecast for the second practice session later Friday.
By JIM ARMSTRONG, Associated Press