The top two were pushed all the way in the second session by Britain's Jenson Button who wound up a superb third fastest in his BMW-powered Williams.
Button, in his first Grand Prix on Suzuka's unique figure-of-eight lay-out, was just 0.2sec off Hakkinen's pace and could have gone fastest but for one problem at a chicane.
Rubens Barrichello was fourth-fastest for Ferrari with Ralf Schumacher - who did displace Hakkinen only to see the time scrapped because he cut the last chicane - fifth in his Williams.
David Coulthard was sixth-fastest for McLaren having suffered one long trip across the gravel earlier while the circuit also caught out the BAR's of Jacques Villeneuve and Ricardo Zonta.
Eddie Irvine, who came so close to winning the drivers' title for Ferrari at Suzuka last year, was eighth for Jaguar Racing with outgoing team-mate Johnny Herbert back in 14th spot.
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