The Finn kept the pressure on his McLaren rivals by lapping the scenic Speedway, overlooked by Japan's Mount Fuji and hosting a grand prix for the first time since 1977, in one minute 19.333 seconds.
Brazilian team mate Felipe Massa, whose slender title hopes could finally fade away this weekend, was 0.379 slower in second place on a bright morning at a circuit notorious for fickle weather conditions.
McLaren's double world champion Fernando Alonso was third quickest, 0.548 off Raikkonen's pace, with championship leading team mate Lewis Hamilton.
Hamilton leads Spaniard Alonso by two points with three races remaining while Raikkonen, who led Massa in a Ferrari one-two at the previous Belgian Grand Prix, is 13 points behind the 22-year-old British rookie.
RECENT FORM
Germany's Nico Rosberg continued his strong recent form with the fifth fastest time in his Toyota-powered Williams with Poland's Robert Kubica sixth for BMW Sauber and Austrian Alex Wurz seventh for Williams.
Williams are chasing Renault for third place in the constructors' championship, with the outgoing champions 11 points ahead but having stopped developing their car to focus on building a better one for 2008.
Ferrari have already won the title after McLaren were stripped of their 2007 constructors' points and fined a record $100 million for having Ferrari technical information in their possession.
German rookie Adrian Sutil, one of the few drivers to have prior experience of racing at Fuji from his days in Japanese Formula Three, was a strong ninth for Spyker.
Briton Anthony Davidson gave Super Aguri a solid start to their home race with 10th fastest time while Japanese team mate Takuma Sato was 17th after spending the first hour in the garage with a mechanical problem.
