Fisichella, teammate of Spaniard Fernando Alonso who is defending his Drivers Championship title, lapped in 1:34.337 on a track that was drying out after rain in the morning.
Brazilian Felipe Massa, driving for Renault rivals Ferrari, was second fastest around the Japan circuit, ahead of his teammate and title leader Michael Schumacher.
"We have only got a flavour of the situation after this session, so it is hard to judge anything at all," said Schumacher, who has won six times at Suzuka.
"We got a little bit of a picture, but not much more.
"As for qualifying, I think we will be fighting Renault for the top places on the grid."
Alonso, who is equal on points with Schumacher with two races remaining in the season was satisfied with his practice time – the fourth fastest on the day.
"This was a normal Friday for me," Alonso said.
"We did very little running because of the conditions but the R26 (car) felt good although there was a bit too much understeer everywhere."
"Every single person at Renault is fighting to the maximum to win the championship," added Alonso.
37-year-old Schumacher can win the 2006 title this weekend if he wins the Japan Grand Prix and Alonso fails to score any points, even with one race remaining in Brazil.