Stoner topped the timesheet with 1 min 59.607 seconds on just his second lap of the day while Honda teammate Dani Pedrosa clocked a third-best 2:00.256.

  MotoGP’s record on the Malaysian circuit was logged in 2009 by seven-time world champion Valentino Rossi, who clocked 2:00.518 while riding an 800cc bike.

  Although quicker, Stoner’s time does not count as an official MotoGP track record as it was not achieved in normal competition.

  MotoGP is switching this year to 1,000cc engines and the three days of pre-season testing in Sepang have given top riders their chance to cut loose on the new bikes against world-class competition.

  Spanish rider Pedrosa said some problems still needed to be ironed out, saying he faced chatter problems with his bike especially on corners as his team experimented with suspension and tyre pressure settings.

  “You go into the corner and the bike is chattering. Chatter is something very difficult to fix. Surely they (Honda) are on it,” he told reporters.

  Yamaha’s Jorge Lorenzo was second on the timesheet, 0.591 seconds off Stoner’s pace while his American teammate Ben Spies crashed while testing a new chassis but emerged unscathed to post the fourth fastest time of 2:00.495.

  On Wednesday, Stoner shrugged off a back injury and the tough challenge from Yamaha riders to post the quickest time.

  Stoner, who won the championship in 2007 and again last year, had been sidelined on Tuesday’s first day of testing after pulling a back muscle while stretching, but bounced back to post the best time on day two.

  Rossi of Ducati, who is looking to make up for a disappointing 2011 campaign, improved on earlier runs to end fifth at 2:00.824.

  The testing session marked an emotional return for riders to the Sepang circuit for the first time since Honda rider Marco Simoncelli died in a shocking crash at the track in October’s Malaysian MotoGP.

  Riders will return to Sepang for another three-day session beginning February 28. The MotoGP 2012 season will officially start April 8 in Qatar.