Poleman Kobayashi, who inherited the top spot after Ferrari's Antonio Giovinazzi had his best lap deleted for a track limits infringement, made the comments after Brendon Hartley crashed the #8 Toyota GR010 HYBRID on his first lap out of the pits at Raidillon.
Technical director Pascal Vasselon confirmed the crash was "just a classic off on cold tyres, which we know can happen".
Speaking after qualifying, which Kobayashi said "was really tricky" after completing a new tyre run for the first time in the lead up to tomorrow's third round of the 2023 WEC, the #7 Toyota driver predicted that drivers will again have to be extra careful after exiting the pits in the race.
Asked by Autosport for his views on running new tyres, Kobayashi said: "The race is going to happen exactly the same.
"Fingers crossed for everyone to be safe, for myself as well, because we don’t want to lose [it] in that point.
"I think everybody is concerned. Everybody. Not only myself.
"Because it’s crazy dangerous, as you see how many people spinning.
"We are not really amateur, we are professional. We do nothing, just cruising around very smoothly.
"I feel really sorry for this scenario because it's really challenging with this size of tyre, without a blanket in this temperature."
Kobayashi stated that Toyota had "expected this because Spa is always cold" and had previously struggled in pre-season testing at the Belgian trick.
"Once we go to this kind of temperature, it’s challenging," he said. "I mean, we did a winter test, we were struggling a lot on out-laps in the winter test. Nobody around, so it’s okay.
"But here when you go out in Eau Rouge directly with a lot of fast cars around. Hopefully nothing is going to happen tomorrow."
Kobayashi explained that there is incentive for drivers to push on out-laps because there is more time to be made up than at other times.
"You can gain 10 seconds on the track when the tyre is ready, but you can gain 10 seconds on out-lap," he added.
"So I think this is a challenging part now. Which we don’t want to be in endurance races, but now they are here."
Hartley's accident was the second noteworthy crash of the weekend in which cold tyres were a factor, after Diego Alessi's #21 AF Corse Ferrari 488 GTE Evo tagged the sister #54 machine of Thomas Flohr at Radillon in FP2 as the latter was building temperature exiting the pits.
Such was the damage to Alessi's car in the incident, for which he was blamed and caused the session to be stopped prematurely, that a replacement chassis had to be sourced from Italy. It was not ready in time for qualifying, and he will have to serve a 30-second stop-go penalty in the race.
James Calado also damaged his Ferrari 499P LMH in an accident at the Sebring prologue shortly after exiting the pits, with the Briton warning afterwards "there is the possibility of some big crashes this year because we are coming out of the pits on cold tyres".
Vasselon was non-committal when asked if the WEC should U-turn on its tyre heater ban.
He replied: "I am not going to give an opinion, but we cannot be surprised that this kind of thing happens. It is part of the game."
Ferrari's Miguel Molina, who qualified the #50 Ferrari second to Kobayashi, told Autosport that he too found conditions "really difficult".
"We knew that when the temperature is low, we struggle with the cold tyres, you need to be really careful in the out-lap and then gradually going up with the temperature, taking a lot of care," he said.
"It’s quite difficult but at the end it’s the same thing for everyone."
