Honda, which hasn't won its home Japanese MotoGP since 2004, enjoyed a dream start to this year's event, as RC212V riders filled the top four places after Friday practice at Motegi.
Dani Pedrosa, whose 2010 title chances ended with a broken collarbone on the same day of last year's round, led the way with a best lap of 1min 46.790sec - already under the official record.
Team-mate and world championship leader Casey Stoner, fastest in the morning session, finished the day just 0.054sec behind the Spaniard, with the third Repsol Honda of Andrea Dovizioso 0.108sec from the top.
Gresini Honda's Marco Simoncelli, who recently re-signed for 2012, completed the Honda domination in fourth (+0.398sec), with Yamaha's reigning world champion and Stoner's only title rival Jorge Lorenzo best of the rest in fifth (+0.520sec).
Lorenzo's team-mate Ben Spies, who had been sick on the way to Japan, only rode for five laps this afternoon before heading for the medical centre. Spies was the only rider to lap slower in FP2.
Fellow American Nicky Hayden had been an impressive third fastest for Ducati in FP1. He remained the top Ducati in FP2 when he was sixth on the carbon-fibre GP11.1, 0.591sec behind Pedrosa.
Local star Hiroshi Aoyama had a strong second session to claim seventh place, and the top satellite bike rider, for Gresini Honda, with Hayden's team-mate Valentino Rossi the first rider over one-second from Pedrosa in eighth place.
Rossi, tenth this morning, is starting his second event with the aluminium section on the front of his Ducati.
Hector Barbera (Aspar) and Colin Edwards (Tech 3) completed the top ten, with Alvaro Bautista eleventh for Suzuki.
Then came Spies, Randy de Puniet (Pramac) and rookie Cal Crutchlow (Tech 3), with Toni Elias (LCR) and Karel Abraham (Cardion AB) the last of the full time riders.
Honda test riders Shinichi Ito and Kosuke Akiyoshi have got wild-card rides for their home round, while Damian Cudlin is making his MotoGP debut as a replacement for the injured Loris Capirossi at Pramac.
Akiyoshi (LCR) was fastest of the trio, lapping 0.159sec slower than Abraham and 2.674sec from Pedrosa. Ito (Honda Racing) was 0.209sec slower with Cudlin, who is making his grand prix debut this weekend, 1.6sec from the former 500cc podium finisher.
Free practice 2:
13. de Puniet