The 24-lap race on Sunday at Motegi was red-flagged at the beginning of the 14th tour owing to heavy rain.
Seconds before the race was stopped, Zarco aquaplaned coming out of the tunnel section into Turn 12 and slid off his Ducati while running in sixth.
Zarco got his bike back to the pitlane within the mandated five-minute limit but was not allowed to take the ultimately aborted restart.
According to Article 1.25.1 of the FIM sporting regulations, "within five minutes after the red flag has been displayed, riders who have not entered the pitlane, crossing the designated pitlane entry timing point together with their motorcycle, will not be classified."
Because Zarco did not technically cross the pitlane entry line and instead pushed his bike back using an adjoining service road next to it, he was unable to take the restart and was therefore not classified in the results.
"I'm OK. I got a good start, but clearly on the first corner I got hit by [Maverick] Vinales who got hit by someone else who I could not see," he said.
"And, fortunately, I did not crash. I came back on track and could see that it was starting rain.
"A few guys stayed on track, but most of the riders came into the pitlane and it was good for me because it was almost a lost race after the first corner.
"Changing the bike and going onto the rain tyres was good for me, because it was not super wet at the beginning and I could catch back a lot of time.
"When the rain came [heavier] it was not easy to understand where the limit was, but I was still fast and catching positions.
"Then after a lot of rain, clearly the red flag was necessary. I crashed just before this red flag because of aquaplaning out of the bridge.
"So, I tried to bring back my bike, I did it but they didn't count my result.
"So, I'm not even finishing in sixth position. I should have crossed the two-metre-wide line of the 60km/h pitlane [entry], and because I have been five metres on the side, they don't count it. So, for this reason I am quite angry."
Had Zarco correctly entered pitlane after his crash, he would have held onto sixth place as the result was taken from lap 12.
