The Spaniard is taking a cautious approach to Sunday's race despite it offering the first of four likely opportunities to wrap up his third world title.
Marquez embarks on the three-race, three-week Asia-Pacific swing through Japan, Australia and Malaysia with a 52-point advantage over Valentino Rossi and 66 points ahead of Jorge Lorenzo in the riders' standings.
With 25 points for a victory, the Spaniard needs to win Sunday's race with Italian Rossi finishing 15th or lower and reigning world champion Lorenzo no better than fourth.
Lorenzo set the fastest time of the day (one minute, 45.151 seconds) in the final minute of Friday's second practice session ahead of Ducati's Andrea Dovizioso (1.45.204), Suzuki rider Maverick Vinales (1.45.248) and Marquez (1.45.303).
Although Marquez comes into the race on the back of a victory in Aragon and has happy memories of the Motegi circuit after clinching his second title there two years ago, the 23-year-old has never won in MotoGP at the home of Honda.
"It's a circuit that has always been a bit challenging for us," Marquez said this week.
"If Aragon was a track that I marked for attacking, Motegi is one that I marked for giving up as few points as possible.
"That said, we'll approach it with an open mentality, aiming for the best result possible but ready to adapt to the circumstances."
Rossi, who won the last of his seven world titles in 2009, was seventh fastest on Friday in 1.45.532.
Marquez was one of several riders who came off their bikes on Friday, sliding off his Honda at turn 10. He was able to rejoin the session.
The weekend of his team mate and compatriot Dani Pedrosa was ended, however, when he high-sided and was sent flying 10 metres onto the trackside, fracturing his right collarbone.
Irishman Eugene Laverty was taken away on a stretcher after a nasty tumble on his Ducati late in the second session but his Aspar team later tweeted that he had walked into the medical centre.
(Writing by Nick Mulvenney in Sydney; Editing by John O'Brien)
