The Australian initially set the pace on Thursday before crashing at the high-speed Turn 14 chicane.
The left side of his Prema car was heavily damaged, though Wharton escaped injury.
Wharton had only completed five laps in the 45-minute session, which was extended due to the red flag.
Campos driver Theophile Nael set the pace on a 1:25.794 just 0.059s ahead of Audi junior Freddie Slater for Trident.
New Zealand’s Louis Sharp was sixth fastest for Prema with a 1:26.175 to end the session 0.381s adrift of Nael.
Formula Regional Oceania champion Ugo Ugochukwu (Campos) was third-fastest ahead of Bruno del Pino (Van Amersfoort) and Pedro Clerot (Rodin).
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“Sorry to my mechanics and sorry to my team,” Wharton wrote on social media.
“Unclear what happened. I had a lot of confidence after the first laps. Need to come back stronger tomorrow.”
Qualifying for the FIA Formula 3 Championship begins at 7:05pm AEST on Friday, which is split into two groups. Sharp will be part of Group A while Wharton will be in Group B.
A BIG impact for James Wharton in FP 😫💥
Thankfully, the Australian climbed out of the car as the fantastic Monaco marshals set to work on the barrier repairs 🛠️#F3 #MonacoGP pic.twitter.com/PJS0EemyJ1
— Formula 3 (@Formula3) June 4, 2026
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