With rain forecast for today, when the final qualifying takes place, Roberts' fastest lap of 1:50.826 could prove good enough to put his Suzuki on pole position for tomorrow's race at the new Motegi twin-ring track.
"I really wanted to get a time in that would be good enough for the front row," the American said. "As soon as I did this lap time I felt that was OK and after that I went into race instead of qualifying mode and started to work on testing different things."
Michael Doohan, the defending champion, was second quickest on a HRC Honda in 1:51.153 while Spain's Carlos Checa, on a Yamaha, was third and John Kocinski fourth fastest, also on a Honda.
Roberts, the eldest son of the three-times 500cc champion Kenny Roberts, surprised some last weekend when he took Suzuki's first 500c win in four years, relegating Doohan, Australia's five-times champion, to fourth place.
However, the 25-year-old, who switched to a rejuvenated Suzuki team after last season on his father's Modenas, had impressed in winter testing and again looked a cut above the rest yesterday with the only time below 1:51.00 on the 4.8-kilometre track.