Martin sets lap record as Marquez struggles at French MotoGP
Ducati-Pramac rider Martin clocked 1min 30.388sec, with Italy's two-time defending world champion Francesco Bagnaia second best 0.145sec behind on a Ducati.
Spanish teenager Pedro Acosta, 19, was third quickest on a GasGas Tech3 following by compatriot Maverick Vinales (Aprilia) and Italian Fabio Di Giannantonio (Ducati-VR46).
Six-time world champion Marquez fell at the start of the session with the Spaniard unable to find his rhythm aboard his Ducati-Gresini.
The 31-year-old finished in 13th position and will have to go through Q1 on Saturday to join the 10 already through to Q2.
The top-10 riders participate directly in Saturday's second qualifying session (Q2) to determine the starting grid for the sprint later in the day and Sunday's race.
"This is the first Friday I've been in trouble," Marquez said. "It happens, we now have to understand the reasons. Today, I fought against the bike.”
Frenchman Fabio Quartararo of Yamaha had the tenth fastest time on his 'home' track under the blazing sunshine in western France.
South African Brad Binder (KTM) finished 17th and will also have to participate in Q1 on Saturday.
The same goes for the Italian Enea Bastianini (11th) whose place in the official Ducati team next season is threatened by Marquez and Martin.
Martin leads the championship with 92 points, closely followed by Bagnaia (75 pts), Bastianini (70), Acosta (69), Maverick Vinales (63) and Marquez (60).